From feead5282c0a155cef823990012c0b63d785357a Mon Sep 17 00:00:00 2001 From: sh-ikeda Date: Fri, 20 Dec 2024 15:29:37 +0900 Subject: [PATCH 1/6] return updated flag --- Rakefile | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Rakefile b/Rakefile index b2771505..5c29aacc 100644 --- a/Rakefile +++ b/Rakefile @@ -577,11 +577,14 @@ namespace :prepare do task :cellosaurus => INPUT_CELLOSAURUS_DIR do $stderr.puts "## Prepare input files for Cellosaurus" download_lock(INPUT_CELLOSAURUS_DIR) do + updated = false input_file = "#{INPUT_CELLOSAURUS_DIR}/cellosaurus.txt" input_url = "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt" if update_input_file?(input_file, input_url) download_file(INPUT_CELLOSAURUS_DIR, input_url) + updated = true end + updated end end @@ -589,12 +592,15 @@ namespace :prepare do task :clinvar => INPUT_CLINVAR_DIR do $stderr.puts "## Prepare input files for ClinVar" download_lock(INPUT_CLINVAR_DIR) do + updated = false input_file = "#{INPUT_CLINVAR_DIR}/variant_summary.txt.gz" input_url = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz" if update_input_file?(input_file, input_url) download_file(INPUT_CLINVAR_DIR, input_url) sh "gzip -dc #{input_file} > #{INPUT_CLINVAR_DIR}/variant_summary.txt" + updated = true end + updated end end From f5e3565f4012b8e0c9982061c488480fad0363c3 Mon Sep 17 00:00:00 2001 From: sh-ikeda Date: Fri, 20 Dec 2024 15:33:23 +0900 Subject: [PATCH 2/6] merge tables --- Rakefile | 13 +++++++++++++ config/bioproject-biosample/config.yaml | 2 +- config/biosample-bioproject/config.yaml | 2 +- 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/Rakefile b/Rakefile index 5c29aacc..45b9c410 100644 --- a/Rakefile +++ b/Rakefile @@ -550,12 +550,22 @@ namespace :prepare do task :bioproject => INPUT_BIOPROJECT_DIR do $stderr.puts "## Prepare input files for BioProject" download_lock(INPUT_BIOPROJECT_DIR) do + updated = false input_file = "#{INPUT_BIOPROJECT_DIR}/bioproject.xml" input_url = "https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml" if update_input_file?(input_file, input_url) download_file(INPUT_BIOPROJECT_DIR, input_url) sh "python bin/bioproject_xml2tsv.py #{INPUT_BIOPROJECT_DIR}/bioproject.xml > #{INPUT_BIOPROJECT_DIR}/bioproject.tsv" + updated = true end + + input_file = "#{INPUT_BIOPROJECT_DIR}/bioproject2biosample.tsv" + input_url = "https://ddbj.nig.ac.jp/public/dblink/bioproject-biosample/bioproject2biosample.tsv" + if update_input_file?(input_file, input_url) + download_file(INPUT_BIOPROJECT_DIR, input_url) + updated = true + end + updated end end @@ -563,13 +573,16 @@ namespace :prepare do task :biosample => INPUT_BIOSAMPLE_DIR do $stderr.puts "## Prepare input files for BioSample" download_lock(INPUT_BIOSAMPLE_DIR) do + updated = false input_file = "#{INPUT_BIOSAMPLE_DIR}/biosample_set.xml.gz" input_url = "https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz" if update_input_file?(input_file, input_url) download_file(INPUT_BIOSAMPLE_DIR, input_url) sh "gzip -dc #{input_file} > #{INPUT_BIOSAMPLE_DIR}/biosample_set.xml" sh "python bin/biosample_xml2tsv.py #{INPUT_BIOSAMPLE_DIR}/biosample_set.xml > #{INPUT_BIOSAMPLE_DIR}/biosample_set.tsv" + updated = true end + updated end end diff --git a/config/bioproject-biosample/config.yaml b/config/bioproject-biosample/config.yaml index 3e5abbbd..e8e2115e 100644 --- a/config/bioproject-biosample/config.yaml +++ b/config/bioproject-biosample/config.yaml @@ -4,4 +4,4 @@ link: reverse: TIO_000095 update: frequency: Monthly - method: curl -sS https://ddbj.nig.ac.jp/public/dblink/bioproject-biosample/bioproject2biosample.tsv + method: awk -F "\t" 'FNR==1{fn++} fn==1{b[$1,$2]=1; print $1 "\t" $2} fn==2&&$2=="ID"{a[$3]=$1} fn==3&&$2=="BioProject ID"&&a[$3]&&!b[a[$3],$1]{print a[$3] "\t" $1}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv diff --git a/config/biosample-bioproject/config.yaml b/config/biosample-bioproject/config.yaml index 3138d637..c6324faf 100644 --- a/config/biosample-bioproject/config.yaml +++ b/config/biosample-bioproject/config.yaml @@ -4,4 +4,4 @@ link: reverse: TIO_000094 update: frequency: Monthly - method: awk -F "\t" 'FNR==NR&&$2=="ID"{a[$3]=$1}FNR!=NR&&$2=="BioProject ID"&&a[$3]{print $1 "\t" a[$3]}' $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv + method: awk -F "\t" 'FNR==1{fn++} fn==1{b[$2,$1]=1; print $2 "\t" $1} fn==2&&$2=="ID"{a[$3]=$1} fn==3&&$2=="BioProject ID"&&a[$3]&&!b[$1,a[$3]]{print $1 "\t" a[$3]}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv From 61c8584e1f97345a6c3923b336fc14961b799e80 Mon Sep 17 00:00:00 2001 From: Toshiaki Katayama Date: Fri, 20 Dec 2024 21:58:15 +0900 Subject: [PATCH 3/6] Updated logs --- log/config-summary.tsv | 4 +- log/error.log | 59 - log/pair_count.tsv | 58 +- log/pair_count_history.tsv | 1 + log/update.log | 3587 ++++++++++++++++-------------------- 5 files changed, 1649 insertions(+), 2060 deletions(-) diff --git a/log/config-summary.tsv b/log/config-summary.tsv index 1746c702..6973a6b7 100644 --- a/log/config-summary.tsv +++ b/log/config-summary.tsv @@ -3,11 +3,11 @@ affy_probeset-ncbigene FIXME Probe Affymetrix probeset http://identifiers.org/af assembly_insdc-bioproject FIXME Genome Assembly INSDC http://identifiers.org/insdc.gca/ nbdc00476 Project BioProject http://identifiers.org/bioproject/ tio:TIO_000078 genome is sequenced in project is sequenced in tio:TIO_000079 project determines genome sequence determines genome sequence Monthly "curl -sS https://ddbj.nig.ac.jp/public/dblink/assembly_genome-bp/assembly_genome2bp.tsv" assembly_insdc-biosample FIXME Genome Assembly INSDC http://identifiers.org/insdc.gca/ nbdc01983 Sample BioSample http://identifiers.org/biosample/ tio:TIO_000080 genome is sequenced with sample is sequenced with tio:TIO_000081 sample is used to sequence genome is used to sequence Monthly "curl -sS https://ddbj.nig.ac.jp/public/dblink/assembly_genome-bs/assembly_genome2bs.tsv" assembly_insdc-insdc_master FIXME Genome Assembly INSDC http://identifiers.org/insdc.gca/ nbdc02567 Project INSDC master http://identifiers.org/insdc/ tio:TIO_000078 genome is sequenced in project is sequenced in tio:TIO_000079 project determines genome sequence determines genome sequence Monthly "curl -sS https://ddbj.nig.ac.jp/public/dblink/assembly_genome-insdc/assembly_genome2insdc.tsv" -bioproject-biosample nbdc00476 Project BioProject http://identifiers.org/bioproject/ nbdc01983 Sample BioSample http://identifiers.org/biosample/ tio:TIO_000094 project analyzes sample analyzes tio:TIO_000095 sample is analyzed in project is analyzed in Monthly "curl -sS https://ddbj.nig.ac.jp/public/dblink/bioproject-biosample/bioproject2biosample.tsv" +bioproject-biosample nbdc00476 Project BioProject http://identifiers.org/bioproject/ nbdc01983 Sample BioSample http://identifiers.org/biosample/ tio:TIO_000094 project analyzes sample analyzes tio:TIO_000095 sample is analyzed in project is analyzed in Monthly "awk -F \"\\t\" 'FNR==1{fn++} fn==1{b[$1,$2]=1; print $1 \"\\t\" $2} fn==2&&$2==\"ID\"{a[$3]=$1} fn==3&&$2==\"BioProject ID\"&&a[$3]&&!b[a[$3],$1]{print a[$3] \"\\t\" $1}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv" bioproject-geo_series nbdc00476 Project BioProject http://identifiers.org/bioproject/ nbdc00080 Project GEO series http://identifiers.org/geo/ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Monthly "awk -F \"\\t\" '$2==\"GEO\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/bioproject/bioproject.tsv" bioproject-pubmed nbdc00476 Project BioProject http://identifiers.org/bioproject/ nbdc00179 Literature PubMed http://rdf.ncbi.nlm.nih.gov/pubmed/ tio:TIO_000032 has reference has reference tio:TIO_000033 is reference of is reference of Monthly "awk -F \"\\t\" '$2==\"PubMed\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/bioproject/bioproject.tsv" bioproject_umbrella-bioproject nbdc00476 Project BioProject umbrella http://identifiers.org/bioproject/ nbdc00476 Project BioProject http://identifiers.org/bioproject/ tio:TIO_000106 has member has member tio:TIO_000107 is member of is member of Monthly "curl -sS https://ddbj.nig.ac.jp/public/dblink/bioproject_umbrella-bioproject/bioproject_umbrella2bioproject.tsv" -biosample-bioproject nbdc01983 Sample BioSample http://identifiers.org/biosample/ nbdc00476 Project BioProject http://identifiers.org/bioproject/ tio:TIO_000095 sample is analyzed in project is analyzed in tio:TIO_000094 project analyzes sample analyzes Monthly "awk -F \"\\t\" 'FNR==NR&&$2==\"ID\"{a[$3]=$1}FNR!=NR&&$2==\"BioProject ID\"&&a[$3]{print $1 \"\\t\" a[$3]}' $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv" +biosample-bioproject nbdc01983 Sample BioSample http://identifiers.org/biosample/ nbdc00476 Project BioProject http://identifiers.org/bioproject/ tio:TIO_000095 sample is analyzed in project is analyzed in tio:TIO_000094 project analyzes sample analyzes Monthly "awk -F \"\\t\" 'FNR==1{fn++} fn==1{b[$2,$1]=1; print $2 \"\\t\" $1} fn==2&&$2==\"ID\"{a[$3]=$1} fn==3&&$2==\"BioProject ID\"&&a[$3]&&!b[$1,a[$3]]{print $1 \"\\t\" a[$3]}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv" biosample-geo_sample nbdc01983 Sample BioSample http://identifiers.org/biosample/ nbdc00080 Sample GEO sample http://identifiers.org/geo/ tio:TIO_000002 is equivalent to is equivalent to tio:TIO_000002 is equivalent to is equivalent to Daily "awk -F \"\\t\" '($2==\"GEO ID\"&&$3~/^GSM[0-9]+$/)||($2==\"GEO URL\"&&$3=gensub(/.+acc=/,\"\",\"g\",$3))&&!a[$1,$3]++{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/biosample/biosample_set.tsv" cellosaurus-ncit_disease nbdc02180 CellLine Cellosaurus http://www.cellosaurus.org/CVCL_ FIXME Phenotype NCIt disease http://purl.obolibrary.org/obo/NCIT_ tio:TIO_000082 cell line is model of phenotype is model of tio:TIO_000083 phenotype is observed in cell line is observed in Quarterly "awk 'BEGIN{RS=\"\\n//\\n\";FS=\"\\n\"}{ncit=\"\";for(i=1;i<=NF;i++){if($i~/^AC/){ac=substr($i,11)}if($i~/^DI NCIt;/){split($i,b,\"; \");ncit=b[2]}}if(ncit)print ac \"\\t\" ncit}' $TOGOID_ROOT/input/cellosaurus/cellosaurus.txt" cellosaurus-orphanet_phenotype nbdc02180 CellLine Cellosaurus http://www.cellosaurus.org/CVCL_ nbdc01422 Phenotype Orphanet phenotype http://identifiers.org/orphanet.ordo/Orphanet_ tio:TIO_000082 cell line is model of phenotype is model of tio:TIO_000083 phenotype is observed in cell line is observed in Quarterly "awk 'BEGIN{RS=\"\\n//\\n\";FS=\"\\n\"}{ordo=\"\";for(i=1;i<=NF;i++){if($i~/^AC/){ac=substr($i,11)}if($i~/^DI ORDO;/){split($i,b,\"; \");ordo=substr(b[2],10)}}if(ordo)print ac \"\\t\" ordo}' $TOGOID_ROOT/input/cellosaurus/cellosaurus.txt" diff --git a/log/error.log b/log/error.log index 2be106fc..765f8a3e 100644 --- a/log/error.log +++ b/log/error.log @@ -1,72 +1,13 @@ Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data): no time information in "" Error: Remote file is empty -# Error: output/tsv/affy_probeset-ncbigene.tsv new file size per old 248 / 314378 = 0.000788859271323057 < 0.5 -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML 503 Service Unavailable -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

Service Unavailable

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

The server is temporarily unable to service your -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML 503 Service Unavailable -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

Service Unavailable

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

The server is temporarily unable to service your -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/assembly_insdc-bioproject.tsv new file size per old 0 / 58955319 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-bioproject.tsv or created file was empty -# Error: output/tsv/assembly_insdc-biosample.tsv new file size per old 0 / 60555966 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-biosample.tsv or created file was empty -# Error: output/tsv/assembly_insdc-insdc_master.tsv new file size per old 0 / 63716447 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-insdc_master.tsv or created file was empty -# Error: output/tsv/bioproject-biosample.tsv new file size per old 0 / 63710867 = 0.0 < 0.5 -# Error: Failed to create output/tsv/bioproject-biosample.tsv or created file was empty -# Error: output/tsv/bioproject_umbrella-bioproject.tsv new file size per old 0 / 2475955 = 0.0 < 0.5 -# Error: Failed to create output/tsv/bioproject_umbrella-bioproject.tsv or created file was empty # Error: output/tsv/chembl_target-ensembl_gene.tsv new file size per old 0 / 61845 = 0.0 < 0.5 # Error: Failed to create output/tsv/chembl_target-ensembl_gene.tsv or created file was empty -# Error: output/tsv/ensembl_gene-ensembl_protein.tsv new file size per old 0 / 493740466 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ensembl_protein.tsv or created file was empty -# Error: output/tsv/ensembl_gene-ensembl_transcript.tsv new file size per old 0 / 606499011 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ensembl_transcript.tsv or created file was empty -# Error: output/tsv/ensembl_gene-ncbigene.tsv new file size per old 0 / 425488063 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ncbigene.tsv or created file was empty -# Error: output/tsv/ensembl_gene-uniprot.tsv new file size per old 0 / 159598297 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-uniprot.tsv or created file was empty -# Error: output/tsv/ensembl_protein-ensembl_transcript.tsv new file size per old 0 / 493651516 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_protein-ensembl_transcript.tsv or created file was empty -# Error: output/tsv/ensembl_transcript-go.tsv new file size per old 0 / 1491765002 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_transcript-go.tsv or created file was empty -# Error: output/tsv/ensembl_transcript-refseq_rna.tsv new file size per old 0 / 1283309099 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_transcript-refseq_rna.tsv or created file was empty -# Error: output/tsv/gea-bioproject.tsv new file size per old 0 / 3032 = 0.0 < 0.5 -# Error: Failed to create output/tsv/gea-bioproject.tsv or created file was empty -# Error: output/tsv/gea-biosample.tsv new file size per old 0 / 121104 = 0.0 < 0.5 -# Error: Failed to create output/tsv/gea-biosample.tsv or created file was empty Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C11%2C10%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5Ba2122h-1b_1-5_2%2ANCC%2F3%3DO%5D%5Ba1221m-1a_1-5%5D%2F1-2-3-2-3-2-3-4-2-3-2%2Fa4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g3-h1_g4-i1_i3-j1_j4-k1&rootnode=true G64227KZ # Error: output/tsv/glycomotif-glytoucan.tsv new file size per old 0 / 2804382 = 0.0 < 0.5 # Error: Failed to create output/tsv/glycomotif-glytoucan.tsv or created file was empty # Error: output/tsv/glytoucan-doid.tsv new file size per old 0 / 4376 = 0.0 < 0.5 # Error: Failed to create output/tsv/glytoucan-doid.tsv or created file was empty # Error: output/tsv/hgnc-ccds.tsv new file size per old 252491 / 544502 = 0.46370995882476096 < 0.5 -# Error: output/tsv/insdc-bioproject.tsv new file size per old 0 / 1191557755 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc-bioproject.tsv or created file was empty -# Error: output/tsv/insdc-biosample.tsv new file size per old 0 / 4269980335 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc-biosample.tsv or created file was empty -# Error: output/tsv/insdc_master-bioproject.tsv new file size per old 0 / 41801168 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc_master-bioproject.tsv or created file was empty -# Error: output/tsv/insdc_master-biosample.tsv new file size per old 0 / 43765492 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc_master-biosample.tsv or created file was empty -# Error: output/tsv/jga_study-jga_dataset.tsv new file size per old 0 / 4378 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-jga_dataset.tsv or created file was empty -# Error: output/tsv/jga_study-nbdc_human_db.tsv new file size per old 0 / 5795 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-nbdc_human_db.tsv or created file was empty -# Error: output/tsv/jga_study-pubmed.tsv new file size per old 0 / 2597 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-pubmed.tsv or created file was empty # Error: output/tsv/lipidmaps-chebi.tsv new file size per old 148 / 253350 = 0.000584172093941188 < 0.5 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML 403 Forbidden diff --git a/log/pair_count.tsv b/log/pair_count.tsv index 93965b12..e2d24955 100644 --- a/log/pair_count.tsv +++ b/log/pair_count.tsv @@ -2,14 +2,14 @@ affy_probeset-ncbigene.tsv 19063 assembly_insdc-bioproject.tsv 2283159 assembly_insdc-biosample.tsv 2225812 assembly_insdc-insdc_master.tsv 2150193 -bioproject-biosample.tsv 2546485 -bioproject-geo_series.tsv 221856 -bioproject-pubmed.tsv 283298 +bioproject-biosample.tsv 21326211 +bioproject-geo_series.tsv 222154 +bioproject-pubmed.tsv 283572 bioproject_umbrella-bioproject.tsv 104586 -biosample-bioproject.tsv 20508479 -biosample-geo_sample.tsv 9590138 -cellosaurus-ncit_disease.tsv 75821 -cellosaurus-orphanet_phenotype.tsv 41448 +biosample-bioproject.tsv 21326211 +biosample-geo_sample.tsv 9592752 +cellosaurus-ncit_disease.tsv 76763 +cellosaurus-orphanet_phenotype.tsv 41988 chebi-glytoucan.tsv 10615 chebi-inchi_key.tsv 175447 chembl_compound-chebi.tsv 34347 @@ -34,13 +34,13 @@ chembl_target-uniprot-TIO_000002.tsv 9094 chembl_target-uniprot-TIO_000130.tsv 1533 chembl_target-uniprot-TIO_000132.tsv 1434 chembl_target-uniprot.tsv 9094 -clinvar-dbsnp.tsv 2937893 -clinvar-hgnc.tsv 3069553 -clinvar-medgen.tsv 4211502 -clinvar-mondo.tsv 2001782 -clinvar-ncbigene.tsv 3069873 -clinvar-omim_phenotype.tsv 1647115 -clinvar-orphanet_phenotype.tsv 1872043 +clinvar-dbsnp.tsv 2937853 +clinvar-hgnc.tsv 3073116 +clinvar-medgen.tsv 4219572 +clinvar-mondo.tsv 2007959 +clinvar-ncbigene.tsv 3073436 +clinvar-omim_phenotype.tsv 1650719 +clinvar-orphanet_phenotype.tsv 1876752 clinvar-uniprot.tsv 20800 cog-insdc.tsv 115826 cog-refseq_protein.tsv 3340026 @@ -119,9 +119,9 @@ medgen-omim_phenotype.tsv 11369 medgen-orphanet_phenotype.tsv 9044 mgi_gene-ensembl_gene.tsv 56426 mgi_gene-hgnc.tsv 24584 -mgi_gene-mgi_allele.tsv 112260 +mgi_gene-mgi_allele.tsv 112305 mgi_gene-ncbigene.tsv 90618 -mgi_gene-uniprot.tsv 79070 +mgi_gene-uniprot.tsv 79092 mgi_genotype-doid.tsv 7844 mgi_genotype-mgi_allele.tsv 125076 mgi_genotype-mp.tsv 401601 @@ -132,22 +132,22 @@ mondo-mesh.tsv 8352 mondo-omim_phenotype.tsv 9693 mondo-orphanet_phenotype.tsv 10380 nando-mondo.tsv 2390 -ncbigene-ensembl_gene.tsv 11755401 -ncbigene-ensembl_protein.tsv 13509818 -ncbigene-ensembl_transcript.tsv 14158040 +ncbigene-ensembl_gene.tsv 11745187 +ncbigene-ensembl_protein.tsv 13481840 +ncbigene-ensembl_transcript.tsv 14087936 ncbigene-flybase_gene.tsv 25078 -ncbigene-go.tsv 102800883 +ncbigene-go.tsv 102899249 ncbigene-hgnc.tsv 43859 ncbigene-mgi_gene.tsv 71682 ncbigene-mirbase.tsv 17541 -ncbigene-omim_gene.tsv 18562 -ncbigene-refseq_genomic.tsv 211772 -ncbigene-refseq_protein.tsv 69891186 -ncbigene-refseq_rna.tsv 67763645 +ncbigene-omim_gene.tsv 18576 +ncbigene-refseq_genomic.tsv 211771 +ncbigene-refseq_protein.tsv 69884551 +ncbigene-refseq_rna.tsv 67904058 ncbigene-rgd.tsv 77241 ncbigene-sgd.tsv 6471 ncbigene-tair.tsv 32835 -ncbigene-taxonomy.tsv 57932960 +ncbigene-taxonomy.tsv 57863025 ncbigene-vgnc.tsv 112163 ncbigene-wormbase_gene.tsv 28785 ncbigene-xenbase_gene.tsv 46840 @@ -170,7 +170,7 @@ pdb-interpro.tsv 726658 pdb-pdb_ccd.tsv 530587 pdb-pfam.tsv 339565 pdb-uniprot.tsv 341431 -pmc-pubmed.tsv 9722361 +pmc-pubmed.tsv 9739099 prosite-prosite_prorule.tsv 1459 pubchem_compound-atc.tsv 4965 pubchem_compound-chebi.tsv 174843 @@ -195,7 +195,7 @@ reactome_reaction-go.tsv 3318 reactome_reaction-iuphar_ligand.tsv 14709 reactome_reaction-mirbase.tsv 194 reactome_reaction-uniprot.tsv 683457 -refseq_protein-uniprot.tsv 175209073 +refseq_protein-uniprot.tsv 175222296 refseq_rna-dbsnp.tsv 267033326 refseq_rna-hgnc.tsv 227308 refseq_rna-ncbigene.tsv 66957414 @@ -230,7 +230,7 @@ sra_sample-biosample.tsv 32441420 swisslipids-chebi.tsv 4276 swisslipids-hmdb.tsv 26026 swisslipids-inchi_key.tsv 593209 -taxonomy-pubmed.tsv 50715 +taxonomy-pubmed.tsv 50757 togovar-clinvar.tsv 781585 togovar-dbsnp.tsv 66877211 togovar-ensembl_gene.tsv 72473309 @@ -270,4 +270,4 @@ wikipathways-hmdb.tsv 4131 wikipathways-lipidmaps.tsv 1429 wikipathways-ncbigene.tsv 30267 wikipathways-uniprot.tsv 33518 -total 5320359597 +total 5340075365 diff --git a/log/pair_count_history.tsv b/log/pair_count_history.tsv index e26eedfb..dedb07f9 100644 --- a/log/pair_count_history.tsv +++ b/log/pair_count_history.tsv @@ -69,3 +69,4 @@ Date affy_probeset-ncbigene assembly_insdc-bioproject assembly_insdc-biosample a 2024-12-01 19063 2283159 2225812 2150193 2546485 220795 282342 104586 20396501 9554924 75821 41448 10615 175447 34347 3101919 3101919 4931 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 9094 9094 1533 1434 2937861 3066621 4205873 1997764 3066941 1643410 1868752 20799 115826 3340026 4019 4849 5671 55423 12969337 15910019 47792 14749031 5546630 12969340 241195 55211171 241612 40165483 141 5046 155799 290 1270 82906 82906 402 310 35510 2121 41201 43839 21140 1325 24074 1912 43753 17345 35045 13532 28712 18945 20374 13701 217899 522 104230 275237 8814 220065 137689 113135 59409158 193975949 1533582 1533178 30269 1679206 22308 1282 116156 479226 1274 787874156 199 305 130 12929 48152 12349 137319849 6318 18747 17044 22699 7334 11369 9044 56426 24584 112132 90618 79070 7844 125076 401601 10712 574 1486 8352 9693 10380 2390 11788765 13562686 14257220 25078 102598546 43858 71682 17541 18557 211769 69787101 67711060 77241 6471 32835 57849022 112163 28785 46840 27178 27199 2533621 2925554 5849918 14432954 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 9686203 1459 4965 174843 2372556 10789 69203 119105151 33861 69387 1253395 2877 623594 1267 270070 13144 41304 348 393545 868219 203666 3318 14709 194 679876 154617876 267033326 227308 66957414 190999 6311722 58133044 66987567 216654 7719 4448 142680 1511 42384671 542643 32363187 329302 36336095 628309 41154297 35034099 31872172 32197530 32216693 32216416 542662 33756784 34098040 34123060 34114079 34116949 32377606 4276 26026 593209 50711 745335 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10340 66728 41313492 9647701 9863257 9863257 590661858 82519 269942826 237103 13525491 7583382 16357 7263 7996 400528 282944 46026396 254254987 254254987 733559 190 790497 5929 1153 4131 1429 30267 33518 5297665623 2024-12-07 19063 2283159 2225812 2150193 2546485 221334 282694 104586 20439564 9573846 75821 41448 10615 175447 34347 3101919 3101919 4931 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 9094 9094 1533 1434 2937889 3068652 4210198 2001160 3068972 1646702 1871572 20800 115826 3340026 4019 4849 5671 55423 12969337 15910019 47792 14749031 5546630 12969340 241195 55211171 241612 40165483 141 5046 155799 290 1270 82906 82906 402 310 35510 2121 41201 43839 21140 1325 24077 1912 43753 17348 35052 13532 28712 18945 20374 13701 217899 522 104230 275237 8814 220065 137689 113135 59409158 193975949 1533582 1533178 30269 1679206 22308 1282 116156 479226 1274 787874156 199 305 130 12929 48152 12349 137319849 6318 18747 17044 22699 7334 11369 9044 56426 24584 112132 90618 79070 7844 125076 401601 10712 574 1486 8352 9693 10380 2390 11788732 13562026 14257155 25078 102596805 43859 71682 17541 18559 211769 69806245 67710490 77241 6471 32835 57866358 112163 28785 46840 27178 27199 2533621 2925554 5849918 14432954 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 9703036 1459 4965 174843 2372556 10789 69203 119107534 33861 69387 1253395 2877 623594 1267 270070 13144 41304 348 393545 868219 203666 3318 14709 194 679876 159946382 267033326 227308 66957414 190999 6311722 58133044 66987567 216654 7719 4448 142680 1511 42384671 543090 32388968 329302 36430485 629932 41251239 35118028 31918768 32226084 32263289 32263012 543109 33803917 34126791 34170279 34161212 34163744 32403387 4276 26026 593209 50709 781585 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10340 66728 41313492 9647701 9863257 9863257 590661858 82519 269942826 237103 13525491 7583382 16357 7263 7996 400528 282944 46026396 254254987 254254987 733559 190 790497 5929 1153 4131 1429 30267 33518 5303878533 2024-12-16 19063 2283159 2225812 2150193 2546485 221856 283298 104586 20508479 9590138 75821 41448 10615 175447 34347 3101919 3101919 4931 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 9094 9094 1533 1434 2937893 3069553 4211502 2001782 3069873 1647115 1872043 20800 115826 3340026 4019 4849 5671 55423 12969337 15910019 47792 14749031 5546630 12969340 241195 55211171 241612 40165483 141 5046 155799 290 1270 70216 82906 402 310 35510 2121 41201 43839 21140 1325 24078 1912 43753 17350 35060 13532 28712 18945 20374 13701 217899 522 104230 275237 8823 220065 139028 114066 59409158 193975949 1533582 1533178 30269 1679206 22308 1282 116156 479226 1274 787874156 199 305 130 12929 48152 12349 137319849 6318 18747 17044 22699 7334 11369 9044 56426 24584 112260 90618 79070 7844 125076 401601 10712 574 1486 8352 9693 10380 2390 11755401 13509818 14158040 25078 102800883 43859 71682 17541 18562 211772 69891186 67763645 77241 6471 32835 57932960 112163 28785 46840 27181 27199 2533621 2925554 5849918 14432954 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 9722361 1459 4965 174843 2372556 10789 69203 119108895 33861 69387 1253395 2877 623594 1267 270398 13144 41304 348 393545 871849 204183 3318 14709 194 683457 175209073 267033326 227308 66957414 190999 6311722 58133044 66987567 216654 7719 4448 142680 1511 42384671 543595 32427001 329302 36544800 632118 41367694 35257303 31968733 32265671 32313254 32312977 543614 33855800 34166458 34222772 34213095 34213846 32441420 4276 26026 593209 50715 781585 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10340 66728 41313492 9647701 9863257 9863257 590661858 82519 269942826 237103 13525491 7583382 16357 7263 7996 400528 282944 46026396 254254987 254254987 733559 190 790497 5929 1153 4131 1429 30267 33518 5320359597 +2024-12-20 19063 2283159 2225812 2150193 21326211 222154 283572 104586 21326211 9592752 76763 41988 10615 175447 34347 3101919 3101919 4931 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 9094 9094 1533 1434 2937853 3073116 4219572 2007959 3073436 1650719 1876752 20800 115826 3340026 4019 4849 5671 55423 12969337 15910019 47792 14749031 5546630 12969340 241195 55211171 241612 40165483 141 5046 155799 290 1270 70216 82906 402 310 35510 2121 41201 43839 21140 1325 24078 1912 43753 17350 35060 13532 28712 18945 20374 13701 217899 522 104230 275237 8823 220065 139028 114066 59409158 193975949 1533582 1533178 30269 1679206 22308 1282 116156 479226 1274 787874156 199 305 130 12929 48152 12349 137319849 6318 18747 17044 22699 7334 11369 9044 56426 24584 112305 90618 79092 7844 125076 401601 10712 574 1486 8352 9693 10380 2390 11745187 13481840 14087936 25078 102899249 43859 71682 17541 18576 211771 69884551 67904058 77241 6471 32835 57863025 112163 28785 46840 27181 27199 2533621 2925554 5849918 14432954 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 9739099 1459 4965 174843 2372556 10789 69203 119108895 33861 69387 1253395 2877 623594 1267 270398 13144 41304 348 393545 871849 204183 3318 14709 194 683457 175222296 267033326 227308 66957414 190999 6311722 58133044 66987567 216654 7719 4448 142680 1511 42384671 543595 32427001 329302 36544800 632118 41367694 35257303 31968733 32265671 32313254 32312977 543614 33855800 34166458 34222772 34213095 34213846 32441420 4276 26026 593209 50757 781585 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10340 66728 41313492 9647701 9863257 9863257 590661858 82519 269942826 237103 13525491 7583382 16357 7263 7996 400528 282944 46026396 254254987 254254987 733559 190 790497 5929 1153 4131 1429 30267 33518 5340075365 diff --git a/log/update.log b/log/update.log index 93043c15..5f5ee5cf 100644 --- a/log/update.log +++ b/log/update.log @@ -1,16 +1,20 @@ -*** Started: 2024-12-15T21:57:19 *** +*** Started: 2024-12-20T17:00:15 *** ## Prepare input files for BioProject # Checking lock file input/bioproject/download.lock for download -# Local file time: 2024-12-12 19:34:24 +0900 (input/bioproject/bioproject.xml) -# Remote file time: 2024-12-15 10:15:21 +0000 (https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml) +# Local file time: 2024-12-15 19:15:21 +0900 (input/bioproject/bioproject.xml) +# Remote file time: 2024-12-19 10:15:31 +0000 (https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/bioproject https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml python bin/bioproject_xml2tsv.py input/bioproject/bioproject.xml > input/bioproject/bioproject.tsv +# Local file time: 2024-03-18 07:00:13 +0900 (input/bioproject/bioproject2biosample.tsv) +# Remote file time: 2024-03-17 22:00:13 +0000 (https://ddbj.nig.ac.jp/public/dblink/bioproject-biosample/bioproject2biosample.tsv) +# Local file size: 63710867 (input/bioproject/bioproject2biosample.tsv) +# Remote file size: 63710867 (https://ddbj.nig.ac.jp/public/dblink/bioproject-biosample/bioproject2biosample.tsv) # Overwriting timestamp of the input/bioproject/download.lock ## Prepare input files for BioSample # Checking lock file input/biosample/download.lock for download -# Local file time: 2024-12-12 23:36:05 +0900 (input/biosample/biosample_set.xml.gz) -# Remote file time: 2024-12-14 14:57:02 +0000 (https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz) +# Local file time: 2024-12-14 23:57:02 +0900 (input/biosample/biosample_set.xml.gz) +# Remote file time: 2024-12-16 14:36:19 +0000 (https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/biosample https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz gzip -dc input/biosample/biosample_set.xml.gz > input/biosample/biosample_set.xml python bin/biosample_xml2tsv.py input/biosample/biosample_set.xml > input/biosample/biosample_set.tsv @@ -18,26 +22,28 @@ python bin/biosample_xml2tsv.py input/biosample/biosample_set.xml > input/biosam ## Prepare input files for Cellosaurus # Checking lock file input/cellosaurus/download.lock for download # Local file time: 2024-09-10 19:57:24 +0900 (input/cellosaurus/cellosaurus.txt) -# Remote file time: 2024-09-10 10:57:24 +0000 (https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt) -# Local file size: 111976636 (input/cellosaurus/cellosaurus.txt) -# Remote file size: 111976636 (https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt) -# Preserving timestamp of the input/cellosaurus/download.lock +# Remote file time: 2024-12-19 10:02:00 +0000 (https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt) +wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/cellosaurus https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt +# Overwriting timestamp of the input/cellosaurus/download.lock ## Prepare input files for ClinVar # Checking lock file input/clinvar/download.lock for download -# Local file time: 2024-12-02 04:53:33 +0900 (input/clinvar/variant_summary.txt.gz) -# Remote file time: 2024-12-08 18:05:10 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz) +# Local file time: 2024-12-09 03:05:10 +0900 (input/clinvar/variant_summary.txt.gz) +# Remote file time: 2024-12-16 02:13:05 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/clinvar https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz gzip -dc input/clinvar/variant_summary.txt.gz > input/clinvar/variant_summary.txt # Overwriting timestamp of the input/clinvar/download.lock ## Prepare input files for Ensembl # Checking lock file input/ensembl/download.lock for download -# File input/ensembl/taxonomy.txt is created 2.2046543105198495 days ago (will be updated when >5 days) -# Preserving timestamp of the input/ensembl/download.lock +# File input/ensembl/taxonomy.txt is created 6.998895552097304 days ago (will be updated when >5 days) +sparql_csv2tsv.sh input/ensembl/taxonomy.rq https://rdfportal.org/ebi/sparql > input/ensembl/taxonomy.txt +# Overwriting timestamp of the input/ensembl/download.lock ## Prepare input files for GlyTouCan # Checking lock file input/glytoucan/download.lock for download -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/glytoucan https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv -sparql_csv2tsv.sh bin/sparql/glycogene-uniprot.rq https://ts.glycosmos.org/sparql > input/glytoucan/glycogene-uniprot.tsv -# Overwriting timestamp of the input/glytoucan/download.lock +# Local file time: 2024-11-27 10:29:54 +0900 (input/glytoucan/glycosmos_ggdbs_pubmed.csv) +# Remote file time: 2024-11-27 01:29:54 +0000 (https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv) +# Local file size: 74413 (input/glytoucan/glycosmos_ggdbs_pubmed.csv) +# Remote file size: 74413 (https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv) +# Preserving timestamp of the input/glytoucan/download.lock ## Prepare input files for HMDB # Checking lock file input/hmdb/download.lock for download # Local file time: 2021-11-18 04:54:48 +0900 (input/hmdb/hmdb_metabolites.zip) @@ -47,10 +53,11 @@ sparql_csv2tsv.sh bin/sparql/glycogene-uniprot.rq https://ts.glycosmos.org/sparq # Preserving timestamp of the input/hmdb/download.lock ## Prepare input files for HGNC # Checking lock file input/hgnc/download.lock for download -# Local file time: 2024-12-03 22:35:33 +0900 (input/hgnc/hgnc_complete_set.txt) +# Local file time: 2024-12-07 01:09:32 +0900 (input/hgnc/hgnc_complete_set.txt) # Remote file time: 2024-12-06 16:09:32 +0000 (https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/hgnc https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt -# Overwriting timestamp of the input/hgnc/download.lock +# Local file size: 16505142 (input/hgnc/hgnc_complete_set.txt) +# Remote file size: 16505142 (https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt) +# Preserving timestamp of the input/hgnc/download.lock ## Prepare input files for Homologene # Checking lock file input/homologene/download.lock for download Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data): no time information in "" @@ -60,14 +67,16 @@ Error: Remote file is empty # Preserving timestamp of the input/homologene/download.lock ## Prepare input files for HP Phenotype # Checking lock file input/hp_phenotype/download.lock for download -# Local file time: 2024-08-13 21:11:36 +0900 (input/hp_phenotype/phenotype.hpoa) +# Local file time: 2024-12-12 09:59:11 +0900 (input/hp_phenotype/phenotype.hpoa) # Remote file time: 2024-12-12 00:59:11 +0000 (http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/hp_phenotype http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa -# Local file time: 2024-08-13 21:11:09 +0900 (input/hp_phenotype/genes_to_phenotype.txt) +# Local file size: 33586642 (input/hp_phenotype/phenotype.hpoa) +# Remote file size: 33586642 (http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa) +# Local file time: 2024-12-12 09:59:09 +0900 (input/hp_phenotype/genes_to_phenotype.txt) # Remote file time: 2024-12-12 00:59:09 +0000 (http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/hp_phenotype http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt +# Local file size: 19657068 (input/hp_phenotype/genes_to_phenotype.txt) +# Remote file size: 19657068 (http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt) bin/sparql_csv2tsv.sh bin/sparql/hp_category.rq https://rdfportal.org/bioportal/sparql > input/hp_phenotype/hp_category.tsv -# Overwriting timestamp of the input/hp_phenotype/download.lock +# Preserving timestamp of the input/hp_phenotype/download.lock ## Prepare input files for COG # Checking lock file input/cog/download.lock for download # Local file time: 2020-09-11 10:37:40 +0900 (input/cog/cog-20.cog.csv) @@ -96,49 +105,49 @@ bin/sparql_csv2tsv.sh bin/sparql/hp_category.rq https://rdfportal.org/bioportal/ # Preserving timestamp of the input/interpro/download.lock ## Prepare input files for MGI_GENE # Checking lock file input/mgi_gene/download.lock for download -# Local file time: 2024-11-25 22:03:48 +0900 (input/mgi_gene/MRK_List2.rpt) -# Remote file time: 2024-12-09 13:01:37 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt) +# Local file time: 2024-12-09 22:01:37 +0900 (input/mgi_gene/MRK_List2.rpt) +# Remote file time: 2024-12-16 13:02:56 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_gene https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt -# Local file time: 2024-11-25 22:01:48 +0900 (input/mgi_gene/MGI_Gene_Model_Coord.rpt) -# Remote file time: 2024-12-09 13:00:46 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_Gene_Model_Coord.rpt) +# Local file time: 2024-12-09 22:00:46 +0900 (input/mgi_gene/MGI_Gene_Model_Coord.rpt) +# Remote file time: 2024-12-16 13:01:08 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_Gene_Model_Coord.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_gene https://www.informatics.jax.org/downloads/reports/MGI_Gene_Model_Coord.rpt -# Local file time: 2024-11-25 22:03:58 +0900 (input/mgi_gene/MRK_SwissProt_TrEMBL.rpt) -# Remote file time: 2024-12-09 13:01:41 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_SwissProt_TrEMBL.rpt) +# Local file time: 2024-12-09 22:01:41 +0900 (input/mgi_gene/MRK_SwissProt_TrEMBL.rpt) +# Remote file time: 2024-12-16 13:03:08 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_SwissProt_TrEMBL.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_gene https://www.informatics.jax.org/downloads/reports/MRK_SwissProt_TrEMBL.rpt -# Local file time: 2024-11-25 22:00:44 +0900 (input/mgi_gene/HGNC_AllianceHomology.rpt) -# Remote file time: 2024-12-09 13:00:26 +0000 (https://www.informatics.jax.org/downloads/reports/HGNC_AllianceHomology.rpt) +# Local file time: 2024-12-09 22:00:26 +0900 (input/mgi_gene/HGNC_AllianceHomology.rpt) +# Remote file time: 2024-12-16 13:00:32 +0000 (https://www.informatics.jax.org/downloads/reports/HGNC_AllianceHomology.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_gene https://www.informatics.jax.org/downloads/reports/HGNC_AllianceHomology.rpt -# Local file time: 2024-11-25 22:03:10 +0900 (input/mgi_gene/MGI_PhenotypicAllele.rpt) -# Remote file time: 2024-12-09 13:01:17 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_PhenotypicAllele.rpt) +# Local file time: 2024-12-09 22:01:17 +0900 (input/mgi_gene/MGI_PhenotypicAllele.rpt) +# Remote file time: 2024-12-16 13:02:15 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_PhenotypicAllele.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_gene https://www.informatics.jax.org/downloads/reports/MGI_PhenotypicAllele.rpt # Overwriting timestamp of the input/mgi_gene/download.lock ## Prepare input files for MGI_GENOTYPE # Checking lock file input/mgi_genotype/download.lock for download -# Local file time: 2024-11-25 22:01:31 +0900 (input/mgi_genotype/MGI_DiseaseGeneModel.rpt) -# Remote file time: 2024-12-09 13:00:42 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_DiseaseGeneModel.rpt) +# Local file time: 2024-12-09 22:00:42 +0900 (input/mgi_genotype/MGI_DiseaseGeneModel.rpt) +# Remote file time: 2024-12-16 13:00:57 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_DiseaseGeneModel.rpt) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/mgi_genotype https://www.informatics.jax.org/downloads/reports/MGI_DiseaseGeneModel.rpt ruby bin/query_mousemine.rb > input/mgi_genotype/mousemine_genotype.tsv # Overwriting timestamp of the input/mgi_genotype/download.lock ## Prepare input files for NCBI Gene # Checking lock file input/ncbigene/download.lock for download -# Local file time: 2024-12-05 21:27:37 +0900 (input/ncbigene/gene2refseq.gz) -# Remote file time: 2024-12-13 09:29:55 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz) +# Local file time: 2024-12-13 18:29:55 +0900 (input/ncbigene/gene2refseq.gz) +# Remote file time: 2024-12-20 06:01:47 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/ncbigene https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz gzip -dc input/ncbigene/gene2refseq.gz > input/ncbigene/gene2refseq -# Local file time: 2024-12-05 21:22:59 +0900 (input/ncbigene/gene2ensembl.gz) -# Remote file time: 2024-12-13 09:25:16 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz) +# Local file time: 2024-12-13 18:25:16 +0900 (input/ncbigene/gene2ensembl.gz) +# Remote file time: 2024-12-20 05:56:29 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/ncbigene https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz gzip -dc input/ncbigene/gene2ensembl.gz > input/ncbigene/gene2ensembl -# Local file time: 2024-12-05 21:24:42 +0900 (input/ncbigene/gene2go.gz) -# Remote file time: 2024-12-13 09:27:00 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz) +# Local file time: 2024-12-13 18:27:00 +0900 (input/ncbigene/gene2go.gz) +# Remote file time: 2024-12-20 05:58:13 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/ncbigene https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz gzip -dc input/ncbigene/gene2go.gz > input/ncbigene/gene2go -# Local file time: 2024-12-05 21:34:46 +0900 (input/ncbigene/Homo_sapiens.gene_info.gz) -# Remote file time: 2024-12-13 09:37:12 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz) +# Local file time: 2024-12-13 18:37:12 +0900 (input/ncbigene/Homo_sapiens.gene_info.gz) +# Remote file time: 2024-12-20 06:09:17 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/ncbigene https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz gzip -dc input/ncbigene/Homo_sapiens.gene_info.gz > input/ncbigene/Homo_sapiens.gene_info -# Local file time: 2024-12-05 21:29:36 +0900 (input/ncbigene/gene_info.gz) -# Remote file time: 2024-12-13 09:31:53 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz) +# Local file time: 2024-12-13 18:31:53 +0900 (input/ncbigene/gene_info.gz) +# Remote file time: 2024-12-20 06:03:58 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/ncbigene https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz gzip -dc input/ncbigene/gene_info.gz > input/ncbigene/gene_info # Overwriting timestamp of the input/ncbigene/download.lock @@ -159,8 +168,8 @@ gzip -dc input/ncbigene/gene_info.gz > input/ncbigene/gene_info # Preserving timestamp of the input/oma_protein/download.lock ## Prepare input files for PMC # Checking lock file input/pmc/download.lock for download -# Local file time: 2024-12-06 19:11:57 +0900 (input/pmc/PMC-ids.csv.gz) -# Remote file time: 2024-12-15 10:17:05 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz) +# Local file time: 2024-12-15 19:17:05 +0900 (input/pmc/PMC-ids.csv.gz) +# Remote file time: 2024-12-20 10:03:34 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/pmc https://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz gzip -dc input/pmc/PMC-ids.csv.gz > input/pmc/PMC-ids.csv # Overwriting timestamp of the input/pmc/download.lock @@ -177,47 +186,59 @@ gzip -dc input/pmc/PMC-ids.csv.gz > input/pmc/PMC-ids.csv # Preserving timestamp of the input/prosite/download.lock ## Prepare input files for Reactome # Checking lock file input/reactome/download.lock for download -# Local file time: 2024-09-29 11:50:03 +0900 (input/reactome/UniProt2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:21:26 +0900 (input/reactome/UniProt2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:21:26 +0000 (https://reactome.org/download/current/UniProt2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/UniProt2ReactomeReactions.txt -# Local file time: 2024-09-29 11:50:56 +0900 (input/reactome/ChEBI2ReactomeReactions.txt) +# Local file size: 96154080 (input/reactome/UniProt2ReactomeReactions.txt) +# Remote file size: 96154080 (https://reactome.org/download/current/UniProt2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:22:21 +0900 (input/reactome/ChEBI2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:22:21 +0000 (https://reactome.org/download/current/ChEBI2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/ChEBI2ReactomeReactions.txt -# Local file time: 2024-09-29 12:10:03 +0900 (input/reactome/Ensembl2ReactomeReactions.txt) +# Local file size: 28800255 (input/reactome/ChEBI2ReactomeReactions.txt) +# Remote file size: 28800255 (https://reactome.org/download/current/ChEBI2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:37:49 +0900 (input/reactome/Ensembl2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:37:49 +0000 (https://reactome.org/download/current/Ensembl2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/Ensembl2ReactomeReactions.txt -# Local file time: 2024-09-29 12:13:26 +0900 (input/reactome/miRBase2ReactomeReactions.txt) +# Local file size: 358390837 (input/reactome/Ensembl2ReactomeReactions.txt) +# Remote file size: 358390837 (https://reactome.org/download/current/Ensembl2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:41:08 +0900 (input/reactome/miRBase2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:41:08 +0000 (https://reactome.org/download/current/miRBase2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/miRBase2ReactomeReactions.txt -# Local file time: 2024-09-29 12:13:22 +0900 (input/reactome/NCBI2ReactomeReactions.txt) +# Local file size: 27061 (input/reactome/miRBase2ReactomeReactions.txt) +# Remote file size: 27061 (https://reactome.org/download/current/miRBase2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:41:03 +0900 (input/reactome/NCBI2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:41:03 +0000 (https://reactome.org/download/current/NCBI2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/NCBI2ReactomeReactions.txt -# Local file time: 2024-09-29 12:13:35 +0900 (input/reactome/GtoP2ReactomeReactions.txt) +# Local file size: 69214978 (input/reactome/NCBI2ReactomeReactions.txt) +# Remote file size: 69214978 (https://reactome.org/download/current/NCBI2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:41:16 +0900 (input/reactome/GtoP2ReactomeReactions.txt) # Remote file time: 2024-11-27 23:41:16 +0000 (https://reactome.org/download/current/GtoP2ReactomeReactions.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/GtoP2ReactomeReactions.txt -# Local file time: 2024-09-29 11:49:33 +0900 (input/reactome/UniProt2Reactome_All_Levels.txt) +# Local file size: 1868064 (input/reactome/GtoP2ReactomeReactions.txt) +# Remote file size: 1868064 (https://reactome.org/download/current/GtoP2ReactomeReactions.txt) +# Local file time: 2024-11-28 08:20:55 +0900 (input/reactome/UniProt2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:20:55 +0000 (https://reactome.org/download/current/UniProt2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/UniProt2Reactome_All_Levels.txt -# Local file time: 2024-09-29 11:50:50 +0900 (input/reactome/ChEBI2Reactome_All_Levels.txt) +# Local file size: 108593551 (input/reactome/UniProt2Reactome_All_Levels.txt) +# Remote file size: 108593551 (https://reactome.org/download/current/UniProt2Reactome_All_Levels.txt) +# Local file time: 2024-11-28 08:22:15 +0900 (input/reactome/ChEBI2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:22:15 +0000 (https://reactome.org/download/current/ChEBI2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/ChEBI2Reactome_All_Levels.txt -# Local file time: 2024-09-29 12:07:44 +0900 (input/reactome/Ensembl2Reactome_All_Levels.txt) +# Local file size: 33148348 (input/reactome/ChEBI2Reactome_All_Levels.txt) +# Remote file size: 33148348 (https://reactome.org/download/current/ChEBI2Reactome_All_Levels.txt) +# Local file time: 2024-11-28 08:35:58 +0900 (input/reactome/Ensembl2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:35:58 +0000 (https://reactome.org/download/current/Ensembl2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/Ensembl2Reactome_All_Levels.txt -# Local file time: 2024-09-29 12:13:25 +0900 (input/reactome/miRBase2Reactome_All_Levels.txt) +# Local file size: 398246897 (input/reactome/Ensembl2Reactome_All_Levels.txt) +# Remote file size: 398246897 (https://reactome.org/download/current/Ensembl2Reactome_All_Levels.txt) +# Local file time: 2024-11-28 08:41:07 +0900 (input/reactome/miRBase2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:41:07 +0000 (https://reactome.org/download/current/miRBase2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/miRBase2Reactome_All_Levels.txt -# Local file time: 2024-09-29 12:12:58 +0900 (input/reactome/NCBI2Reactome_All_Levels.txt) +# Local file size: 43543 (input/reactome/miRBase2Reactome_All_Levels.txt) +# Remote file size: 43543 (https://reactome.org/download/current/miRBase2Reactome_All_Levels.txt) +# Local file time: 2024-11-28 08:40:38 +0900 (input/reactome/NCBI2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:40:38 +0000 (https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt -# Local file time: 2024-09-29 12:13:33 +0900 (input/reactome/GtoP2Reactome_All_Levels.txt) +# Local file size: 77752248 (input/reactome/NCBI2Reactome_All_Levels.txt) +# Remote file size: 77752248 (https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt) +# Local file time: 2024-11-28 08:41:15 +0900 (input/reactome/GtoP2Reactome_All_Levels.txt) # Remote file time: 2024-11-27 23:41:15 +0000 (https://reactome.org/download/current/GtoP2Reactome_All_Levels.txt) -wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/reactome https://reactome.org/download/current/GtoP2Reactome_All_Levels.txt -# Overwriting timestamp of the input/reactome/download.lock +# Local file size: 4818359 (input/reactome/GtoP2Reactome_All_Levels.txt) +# Remote file size: 4818359 (https://reactome.org/download/current/GtoP2Reactome_All_Levels.txt) +# Preserving timestamp of the input/reactome/download.lock ## Prepare input files for RefSeq Protein # Checking lock file input/refseq_protein/download.lock for download -# Local file time: 2024-12-05 19:23:44 +0900 (input/refseq_protein/gene_refseq_uniprotkb_collab.gz) -# Remote file time: 2024-12-12 10:26:06 +0000 (https://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz) +# Local file time: 2024-12-12 19:26:06 +0900 (input/refseq_protein/gene_refseq_uniprotkb_collab.gz) +# Remote file time: 2024-12-19 10:25:56 +0000 (https://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/refseq_protein https://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz # Overwriting timestamp of the input/refseq_protein/download.lock ## Prepare input files for RefSeq RNA @@ -244,8 +265,8 @@ wget --quiet --recursive --no-parent --no-directories --timestamping --no-check- # Preserving timestamp of the input/rhea/download.lock ## Prepare input files for SRA # Checking lock file input/sra/download.lock for download -# Local file time: 2024-12-06 01:08:41 +0900 (input/sra/SRA_Accessions.tab) -# Remote file time: 2024-12-14 16:22:54 +0000 (https://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab) +# Local file time: 2024-12-15 01:22:54 +0900 (input/sra/SRA_Accessions.tab) +# Remote file time: 2024-12-19 16:38:20 +0000 (https://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/sra https://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab # Overwriting timestamp of the input/sra/download.lock ## Prepare input files for SwissLipids @@ -269,541 +290,467 @@ wget --quiet --no-check-certificate -O input/uniprot/uniprot_proteome.tab.gz 'ht # Preserving timestamp of the input/uniprot/download.lock ## Prepare input files for Taxonomy # Checking lock file input/taxonomy/download.lock for download -# Local file time: 2024-12-06 19:29:01 +0900 (input/taxonomy/taxdump.tar.gz) -# Remote file time: 2024-12-15 15:29:19 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz) +# Local file time: 2024-12-16 00:29:19 +0900 (input/taxonomy/taxdump.tar.gz) +# Remote file time: 2024-12-20 10:28:41 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz) wget --quiet --recursive --no-parent --no-directories --timestamping --no-check-certificate --directory-prefix input/taxonomy https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz mkdir -p input/taxonomy/taxdump && tar xzf input/taxonomy/taxdump.tar.gz -C input/taxonomy/taxdump/ # Overwriting timestamp of the input/taxonomy/download.lock ### Update TSV for affy_probeset-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/affy_probeset-ncbigene.tsv is newer than config/affy_probeset-ncbigene/config.yaml # File output/tsv/affy_probeset-ncbigene.tsv has no timestamp file -# File output/tsv/affy_probeset-ncbigene.tsv is created 9.217587901309283 days ago (will be updated when >5 days) +# File output/tsv/affy_probeset-ncbigene.tsv is created 14.010735987905614 days ago (will be updated when >5 days) ## Update config/affy_probeset-ncbigene/config.yaml => output/tsv/affy_probeset-ncbigene.tsv -< 2024-12-16T01:06:15 affy_probeset-ncbigene +< 2024-12-20T20:08:23 affy_probeset-ncbigene togoid-config config/affy_probeset-ncbigene update -# Error: output/tsv/affy_probeset-ncbigene.tsv new file size per old 248 / 314378 = 0.000788859271323057 < 0.5 -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML 503 Service Unavailable -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

Service Unavailable

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

The server is temporarily unable to service your -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML 503 Service Unavailable -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

Service Unavailable

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML

The server is temporarily unable to service your -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity -# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.

-# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML -# Failure: output/tsv/affy_probeset-ncbigene.tsv is not updated -> 2024-12-16T01:06:16 affy_probeset-ncbigene +# Success: output/tsv/affy_probeset-ncbigene.tsv is updated +> 2024-12-20T20:08:25 affy_probeset-ncbigene Rule for TSV (output/tsv/affy_probeset-ncbigene.tsv) ------------------------------ Investigating output/tsv/affy_probeset-ncbigene.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 19:52:56 +0900 +task needed: false +timestamp: 2024-12-20 20:08:25 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for assembly_insdc-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/assembly_insdc-bioproject.tsv is newer than config/assembly_insdc-bioproject/config.yaml # File output/tsv/assembly_insdc-bioproject.tsv has no timestamp file -# File output/tsv/assembly_insdc-bioproject.tsv is created 9.217571553977534 days ago (will be updated when >5 days) +# File output/tsv/assembly_insdc-bioproject.tsv is created 14.01072446645743 days ago (will be updated when >5 days) ## Update config/assembly_insdc-bioproject/config.yaml => output/tsv/assembly_insdc-bioproject.tsv -< 2024-12-16T01:06:16 assembly_insdc-bioproject +< 2024-12-20T20:08:25 assembly_insdc-bioproject togoid-config config/assembly_insdc-bioproject update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/assembly_insdc-bioproject.tsv new file size per old 0 / 58955319 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-bioproject.tsv or created file was empty -# Failure: output/tsv/assembly_insdc-bioproject.tsv is not updated -> 2024-12-16T01:08:24 assembly_insdc-bioproject +# Success: output/tsv/assembly_insdc-bioproject.tsv is updated +> 2024-12-20T20:08:27 assembly_insdc-bioproject Rule for TSV (output/tsv/assembly_insdc-bioproject.tsv) ------------------------------ Investigating output/tsv/assembly_insdc-bioproject.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 19:52:58 +0900 +task needed: false +timestamp: 2024-12-20 20:08:27 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for assembly_insdc-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/assembly_insdc-biosample.tsv is newer than config/assembly_insdc-biosample/config.yaml # File output/tsv/assembly_insdc-biosample.tsv has no timestamp file -# File output/tsv/assembly_insdc-biosample.tsv is created 9.219019775532976 days ago (will be updated when >5 days) +# File output/tsv/assembly_insdc-biosample.tsv is created 14.010728165882824 days ago (will be updated when >5 days) ## Update config/assembly_insdc-biosample/config.yaml => output/tsv/assembly_insdc-biosample.tsv -< 2024-12-16T01:08:24 assembly_insdc-biosample +< 2024-12-20T20:08:27 assembly_insdc-biosample togoid-config config/assembly_insdc-biosample update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/assembly_insdc-biosample.tsv new file size per old 0 / 60555966 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-biosample.tsv or created file was empty -# Failure: output/tsv/assembly_insdc-biosample.tsv is not updated -> 2024-12-16T01:10:31 assembly_insdc-biosample +# Success: output/tsv/assembly_insdc-biosample.tsv is updated +> 2024-12-20T20:08:30 assembly_insdc-biosample Rule for TSV (output/tsv/assembly_insdc-biosample.tsv) ------------------------------ Investigating output/tsv/assembly_insdc-biosample.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 19:53:01 +0900 +task needed: false +timestamp: 2024-12-20 20:08:30 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for assembly_insdc-insdc_master if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/assembly_insdc-insdc_master.tsv is newer than config/assembly_insdc-insdc_master/config.yaml # File output/tsv/assembly_insdc-insdc_master.tsv has no timestamp file -# File output/tsv/assembly_insdc-insdc_master.tsv is created 9.220466882386042 days ago (will be updated when >5 days) +# File output/tsv/assembly_insdc-insdc_master.tsv is created 14.010726679099422 days ago (will be updated when >5 days) ## Update config/assembly_insdc-insdc_master/config.yaml => output/tsv/assembly_insdc-insdc_master.tsv -< 2024-12-16T01:10:31 assembly_insdc-insdc_master +< 2024-12-20T20:08:30 assembly_insdc-insdc_master togoid-config config/assembly_insdc-insdc_master update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/assembly_insdc-insdc_master.tsv new file size per old 0 / 63716447 = 0.0 < 0.5 -# Error: Failed to create output/tsv/assembly_insdc-insdc_master.tsv or created file was empty -# Failure: output/tsv/assembly_insdc-insdc_master.tsv is not updated -> 2024-12-16T01:12:39 assembly_insdc-insdc_master +# Success: output/tsv/assembly_insdc-insdc_master.tsv is updated +> 2024-12-20T20:08:32 assembly_insdc-insdc_master Rule for TSV (output/tsv/assembly_insdc-insdc_master.tsv) ------------------------------ Investigating output/tsv/assembly_insdc-insdc_master.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 19:53:03 +0900 +task needed: false +timestamp: 2024-12-20 20:08:32 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for bioproject-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true -# File output/tsv/bioproject-biosample.tsv is newer than config/bioproject-biosample/config.yaml -# File output/tsv/bioproject-biosample.tsv is older than input/bioproject/download.lock +### Update TSV for bioproject-biosample if check_tsv_filesize false or check_config_timestamp true or check_tsv_timestamp true +# File output/tsv/bioproject-biosample.tsv is older than config/bioproject-biosample/config.yaml ## Update config/bioproject-biosample/config.yaml => output/tsv/bioproject-biosample.tsv -< 2024-12-16T01:12:39 bioproject-biosample +< 2024-12-20T20:08:32 bioproject-biosample togoid-config config/bioproject-biosample update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/bioproject-biosample.tsv new file size per old 0 / 63710867 = 0.0 < 0.5 -# Error: Failed to create output/tsv/bioproject-biosample.tsv or created file was empty -# Failure: output/tsv/bioproject-biosample.tsv is not updated -> 2024-12-16T01:14:46 bioproject-biosample +# Success: output/tsv/bioproject-biosample.tsv is updated +> 2024-12-20T20:10:53 bioproject-biosample Rule for TSV (output/tsv/bioproject-biosample.tsv) ------------------------------ Investigating output/tsv/bioproject-biosample.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 19:53:06 +0900 +timestamp: 2024-12-20 20:10:53 +0900 pre-requisites: --output/tsv/ () ---prepare:bioproject (2024-12-16 01:14:46 +0900) -latest-prerequisite time: 2024-12-16 01:14:46 +0900 +--prepare:bioproject (2024-12-20 20:10:53 +0900) +latest-prerequisite time: 2024-12-20 20:10:53 +0900 ................................ ### Update TSV for bioproject-geo_series if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/bioproject-geo_series.tsv is newer than config/bioproject-geo_series/config.yaml # File output/tsv/bioproject-geo_series.tsv is older than input/bioproject/download.lock ## Update config/bioproject-geo_series/config.yaml => output/tsv/bioproject-geo_series.tsv -< 2024-12-16T01:14:46 bioproject-geo_series +< 2024-12-20T20:10:53 bioproject-geo_series togoid-config config/bioproject-geo_series update # Success: output/tsv/bioproject-geo_series.tsv is updated -> 2024-12-16T01:14:48 bioproject-geo_series +> 2024-12-20T20:10:55 bioproject-geo_series Rule for TSV (output/tsv/bioproject-geo_series.tsv) ------------------------------ Investigating output/tsv/bioproject-geo_series.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:14:48 +0900 +timestamp: 2024-12-20 20:10:55 +0900 pre-requisites: --output/tsv/ () ---prepare:bioproject (2024-12-16 01:14:48 +0900) -latest-prerequisite time: 2024-12-16 01:14:48 +0900 +--prepare:bioproject (2024-12-20 20:10:55 +0900) +latest-prerequisite time: 2024-12-20 20:10:55 +0900 ................................ ### Update TSV for bioproject-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/bioproject-pubmed.tsv is newer than config/bioproject-pubmed/config.yaml # File output/tsv/bioproject-pubmed.tsv is older than input/bioproject/download.lock ## Update config/bioproject-pubmed/config.yaml => output/tsv/bioproject-pubmed.tsv -< 2024-12-16T01:14:48 bioproject-pubmed +< 2024-12-20T20:10:55 bioproject-pubmed togoid-config config/bioproject-pubmed update # Success: output/tsv/bioproject-pubmed.tsv is updated -> 2024-12-16T01:14:50 bioproject-pubmed +> 2024-12-20T20:10:56 bioproject-pubmed Rule for TSV (output/tsv/bioproject-pubmed.tsv) ------------------------------ Investigating output/tsv/bioproject-pubmed.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:14:50 +0900 +timestamp: 2024-12-20 20:10:56 +0900 pre-requisites: --output/tsv/ () ---prepare:bioproject (2024-12-16 01:14:50 +0900) -latest-prerequisite time: 2024-12-16 01:14:50 +0900 +--prepare:bioproject (2024-12-20 20:10:56 +0900) +latest-prerequisite time: 2024-12-20 20:10:56 +0900 ................................ ### Update TSV for bioproject_umbrella-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/bioproject_umbrella-bioproject.tsv is newer than config/bioproject_umbrella-bioproject/config.yaml # File output/tsv/bioproject_umbrella-bioproject.tsv has no timestamp file -# File output/tsv/bioproject_umbrella-bioproject.tsv is created 9.223377438290486 days ago (will be updated when >5 days) +# File output/tsv/bioproject_umbrella-bioproject.tsv is created 14.012344268570532 days ago (will be updated when >5 days) ## Update config/bioproject_umbrella-bioproject/config.yaml => output/tsv/bioproject_umbrella-bioproject.tsv -< 2024-12-16T01:14:50 bioproject_umbrella-bioproject +< 2024-12-20T20:10:56 bioproject_umbrella-bioproject togoid-config config/bioproject_umbrella-bioproject update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/bioproject_umbrella-bioproject.tsv new file size per old 0 / 2475955 = 0.0 < 0.5 -# Error: Failed to create output/tsv/bioproject_umbrella-bioproject.tsv or created file was empty -# Failure: output/tsv/bioproject_umbrella-bioproject.tsv is not updated -> 2024-12-16T01:16:57 bioproject_umbrella-bioproject +# Success: output/tsv/bioproject_umbrella-bioproject.tsv is updated +> 2024-12-20T20:10:57 bioproject_umbrella-bioproject Rule for TSV (output/tsv/bioproject_umbrella-bioproject.tsv) ------------------------------ Investigating output/tsv/bioproject_umbrella-bioproject.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 19:53:10 +0900 +timestamp: 2024-12-20 20:10:57 +0900 pre-requisites: --output/tsv/ () ---prepare:bioproject (2024-12-16 01:16:57 +0900) -latest-prerequisite time: 2024-12-16 01:16:57 +0900 +--prepare:bioproject (2024-12-20 20:10:57 +0900) +latest-prerequisite time: 2024-12-20 20:10:57 +0900 ................................ -### Update TSV for biosample-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true -# File output/tsv/biosample-bioproject.tsv is newer than config/biosample-bioproject/config.yaml -# File output/tsv/biosample-bioproject.tsv is older than input/biosample/download.lock +### Update TSV for biosample-bioproject if check_tsv_filesize false or check_config_timestamp true or check_tsv_timestamp true +# File output/tsv/biosample-bioproject.tsv is older than config/biosample-bioproject/config.yaml ## Update config/biosample-bioproject/config.yaml => output/tsv/biosample-bioproject.tsv -< 2024-12-16T01:16:57 biosample-bioproject +< 2024-12-20T20:10:57 biosample-bioproject togoid-config config/biosample-bioproject update # Success: output/tsv/biosample-bioproject.tsv is updated -> 2024-12-16T01:18:21 biosample-bioproject +> 2024-12-20T20:12:46 biosample-bioproject Rule for TSV (output/tsv/biosample-bioproject.tsv) ------------------------------ Investigating output/tsv/biosample-bioproject.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:18:21 +0900 +timestamp: 2024-12-20 20:12:46 +0900 pre-requisites: --output/tsv/ () ---prepare:biosample (2024-12-16 01:18:21 +0900) -latest-prerequisite time: 2024-12-16 01:18:21 +0900 +--prepare:biosample (2024-12-20 20:12:46 +0900) +latest-prerequisite time: 2024-12-20 20:12:46 +0900 ................................ ### Update TSV for biosample-geo_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/biosample-geo_sample.tsv is newer than config/biosample-geo_sample/config.yaml # File output/tsv/biosample-geo_sample.tsv is older than input/biosample/download.lock ## Update config/biosample-geo_sample/config.yaml => output/tsv/biosample-geo_sample.tsv -< 2024-12-16T01:18:21 biosample-geo_sample +< 2024-12-20T20:12:46 biosample-geo_sample togoid-config config/biosample-geo_sample update # Success: output/tsv/biosample-geo_sample.tsv is updated -> 2024-12-16T01:19:56 biosample-geo_sample +> 2024-12-20T20:14:22 biosample-geo_sample Rule for TSV (output/tsv/biosample-geo_sample.tsv) ------------------------------ Investigating output/tsv/biosample-geo_sample.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:19:56 +0900 +timestamp: 2024-12-20 20:14:22 +0900 pre-requisites: --output/tsv/ () ---prepare:biosample (2024-12-16 01:19:56 +0900) -latest-prerequisite time: 2024-12-16 01:19:56 +0900 +--prepare:biosample (2024-12-20 20:14:22 +0900) +latest-prerequisite time: 2024-12-20 20:14:22 +0900 ................................ -### Update TSV for cellosaurus-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false +### Update TSV for cellosaurus-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/cellosaurus-ncit_disease.tsv is newer than config/cellosaurus-ncit_disease/config.yaml -# File output/tsv/cellosaurus-ncit_disease.tsv is newer than input/cellosaurus/download.lock -# => Preserving output/tsv/cellosaurus-ncit_disease.tsv +# File output/tsv/cellosaurus-ncit_disease.tsv is older than input/cellosaurus/download.lock +## Update config/cellosaurus-ncit_disease/config.yaml => output/tsv/cellosaurus-ncit_disease.tsv +< 2024-12-20T20:14:22 cellosaurus-ncit_disease +togoid-config config/cellosaurus-ncit_disease update +# Success: output/tsv/cellosaurus-ncit_disease.tsv is updated +> 2024-12-20T20:14:27 cellosaurus-ncit_disease Rule for TSV (output/tsv/cellosaurus-ncit_disease.tsv) ------------------------------ Investigating output/tsv/cellosaurus-ncit_disease.tsv class: Rake::FileTask task needed: true -timestamp: 2024-09-13 20:46:20 +0900 +timestamp: 2024-12-20 20:14:27 +0900 pre-requisites: --output/tsv/ () ---prepare:cellosaurus (2024-12-16 01:19:56 +0900) -latest-prerequisite time: 2024-12-16 01:19:56 +0900 +--prepare:cellosaurus (2024-12-20 20:14:27 +0900) +latest-prerequisite time: 2024-12-20 20:14:27 +0900 ................................ -### Update TSV for cellosaurus-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false +### Update TSV for cellosaurus-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/cellosaurus-orphanet_phenotype.tsv is newer than config/cellosaurus-orphanet_phenotype/config.yaml -# File output/tsv/cellosaurus-orphanet_phenotype.tsv is newer than input/cellosaurus/download.lock -# => Preserving output/tsv/cellosaurus-orphanet_phenotype.tsv +# File output/tsv/cellosaurus-orphanet_phenotype.tsv is older than input/cellosaurus/download.lock +## Update config/cellosaurus-orphanet_phenotype/config.yaml => output/tsv/cellosaurus-orphanet_phenotype.tsv +< 2024-12-20T20:14:27 cellosaurus-orphanet_phenotype +togoid-config config/cellosaurus-orphanet_phenotype update +# Success: output/tsv/cellosaurus-orphanet_phenotype.tsv is updated +> 2024-12-20T20:14:31 cellosaurus-orphanet_phenotype Rule for TSV (output/tsv/cellosaurus-orphanet_phenotype.tsv) ------------------------------ Investigating output/tsv/cellosaurus-orphanet_phenotype.tsv class: Rake::FileTask task needed: true -timestamp: 2024-09-13 20:46:24 +0900 +timestamp: 2024-12-20 20:14:31 +0900 pre-requisites: --output/tsv/ () ---prepare:cellosaurus (2024-12-16 01:19:56 +0900) -latest-prerequisite time: 2024-12-16 01:19:56 +0900 +--prepare:cellosaurus (2024-12-20 20:14:31 +0900) +latest-prerequisite time: 2024-12-20 20:14:31 +0900 ................................ -### Update TSV for chebi-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chebi-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chebi-glytoucan.tsv is newer than config/chebi-glytoucan/config.yaml # File output/tsv/chebi-glytoucan.tsv has no timestamp file -# File output/tsv/chebi-glytoucan.tsv is created 9.224166174413218 days ago (will be updated when >5 days) -## Update config/chebi-glytoucan/config.yaml => output/tsv/chebi-glytoucan.tsv -< 2024-12-16T01:19:56 chebi-glytoucan -togoid-config config/chebi-glytoucan update -# Success: output/tsv/chebi-glytoucan.tsv is updated -> 2024-12-16T01:19:56 chebi-glytoucan +# File output/tsv/chebi-glytoucan.tsv is created 4.78790622232338 days ago (will be updated when >5 days) +# => Preserving output/tsv/chebi-glytoucan.tsv Rule for TSV (output/tsv/chebi-glytoucan.tsv) ------------------------------ Investigating output/tsv/chebi-glytoucan.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:19:56 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chebi-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chebi-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chebi-inchi_key.tsv is newer than config/chebi-inchi_key/config.yaml # File output/tsv/chebi-inchi_key.tsv has no timestamp file -# File output/tsv/chebi-inchi_key.tsv is created 9.224156035944839 days ago (will be updated when >5 days) -## Update config/chebi-inchi_key/config.yaml => output/tsv/chebi-inchi_key.tsv -< 2024-12-16T01:19:56 chebi-inchi_key -togoid-config config/chebi-inchi_key update -# Success: output/tsv/chebi-inchi_key.tsv is updated -> 2024-12-16T01:19:57 chebi-inchi_key +# File output/tsv/chebi-inchi_key.tsv is created 4.7878972007009954 days ago (will be updated when >5 days) +# => Preserving output/tsv/chebi-inchi_key.tsv Rule for TSV (output/tsv/chebi-inchi_key.tsv) ------------------------------ Investigating output/tsv/chebi-inchi_key.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:19:57 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-chebi.tsv is newer than config/chembl_compound-chebi/config.yaml # File output/tsv/chembl_compound-chebi.tsv has no timestamp file -# File output/tsv/chembl_compound-chebi.tsv is created 9.224153792202628 days ago (will be updated when >5 days) -## Update config/chembl_compound-chebi/config.yaml => output/tsv/chembl_compound-chebi.tsv -< 2024-12-16T01:19:57 chembl_compound-chebi -togoid-config config/chembl_compound-chebi update -# Success: output/tsv/chembl_compound-chebi.tsv is updated -> 2024-12-16T01:19:57 chembl_compound-chebi +# File output/tsv/chembl_compound-chebi.tsv is created 4.787891326859421 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-chebi.tsv Rule for TSV (output/tsv/chembl_compound-chebi.tsv) ------------------------------ Investigating output/tsv/chembl_compound-chebi.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:19:57 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-chembl_target if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-chembl_target if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-chembl_target.tsv is newer than config/chembl_compound-chembl_target/config.yaml # File output/tsv/chembl_compound-chembl_target.tsv has no timestamp file -# File output/tsv/chembl_compound-chembl_target.tsv is created 9.212816560797663 days ago (will be updated when >5 days) -## Update config/chembl_compound-chembl_target/config.yaml => output/tsv/chembl_compound-chembl_target.tsv -< 2024-12-16T01:19:57 chembl_compound-chembl_target -togoid-config config/chembl_compound-chembl_target update -# Success: output/tsv/chembl_compound-chembl_target.tsv is updated -> 2024-12-16T01:36:09 chembl_compound-chembl_target +# File output/tsv/chembl_compound-chembl_target.tsv is created 4.776643489550509 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-chembl_target.tsv Rule for TSV (output/tsv/chembl_compound-chembl_target.tsv) ------------------------------ Investigating output/tsv/chembl_compound-chembl_target.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:09 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-drugbank.tsv is newer than config/chembl_compound-drugbank/config.yaml # File output/tsv/chembl_compound-drugbank.tsv has no timestamp file -# File output/tsv/chembl_compound-drugbank.tsv is created 9.224059175063415 days ago (will be updated when >5 days) -## Update config/chembl_compound-drugbank/config.yaml => output/tsv/chembl_compound-drugbank.tsv -< 2024-12-16T01:36:09 chembl_compound-drugbank -togoid-config config/chembl_compound-drugbank update -# Success: output/tsv/chembl_compound-drugbank.tsv is updated -> 2024-12-16T01:36:10 chembl_compound-drugbank +# File output/tsv/chembl_compound-drugbank.tsv is created 4.77663843721728 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-drugbank.tsv Rule for TSV (output/tsv/chembl_compound-drugbank.tsv) ------------------------------ Investigating output/tsv/chembl_compound-drugbank.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-hmdb.tsv is newer than config/chembl_compound-hmdb/config.yaml # File output/tsv/chembl_compound-hmdb.tsv has no timestamp file -# File output/tsv/chembl_compound-hmdb.tsv is created 9.224059415284827 days ago (will be updated when >5 days) -## Update config/chembl_compound-hmdb/config.yaml => output/tsv/chembl_compound-hmdb.tsv -< 2024-12-16T01:36:10 chembl_compound-hmdb -togoid-config config/chembl_compound-hmdb update -# Success: output/tsv/chembl_compound-hmdb.tsv is updated -> 2024-12-16T01:36:10 chembl_compound-hmdb +# File output/tsv/chembl_compound-hmdb.tsv is created 4.776633581728021 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-hmdb.tsv Rule for TSV (output/tsv/chembl_compound-hmdb.tsv) ------------------------------ Investigating output/tsv/chembl_compound-hmdb.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-inchi_key.tsv is newer than config/chembl_compound-inchi_key/config.yaml # File output/tsv/chembl_compound-inchi_key.tsv has no timestamp file -# File output/tsv/chembl_compound-inchi_key.tsv is created 9.224005967552095 days ago (will be updated when >5 days) -## Update config/chembl_compound-inchi_key/config.yaml => output/tsv/chembl_compound-inchi_key.tsv -< 2024-12-16T01:36:10 chembl_compound-inchi_key -togoid-config config/chembl_compound-inchi_key update -# Success: output/tsv/chembl_compound-inchi_key.tsv is updated -> 2024-12-16T01:36:14 chembl_compound-inchi_key +# File output/tsv/chembl_compound-inchi_key.tsv is created 4.7765879387818515 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-inchi_key.tsv Rule for TSV (output/tsv/chembl_compound-inchi_key.tsv) ------------------------------ Investigating output/tsv/chembl_compound-inchi_key.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:14 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-mesh.tsv is newer than config/chembl_compound-mesh/config.yaml # File output/tsv/chembl_compound-mesh.tsv has no timestamp file -# File output/tsv/chembl_compound-mesh.tsv is created 9.224046413200751 days ago (will be updated when >5 days) -## Update config/chembl_compound-mesh/config.yaml => output/tsv/chembl_compound-mesh.tsv -< 2024-12-16T01:36:14 chembl_compound-mesh -togoid-config config/chembl_compound-mesh update -# Success: output/tsv/chembl_compound-mesh.tsv is updated -> 2024-12-16T01:36:15 chembl_compound-mesh +# File output/tsv/chembl_compound-mesh.tsv is created 4.7765825162820255 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-mesh.tsv Rule for TSV (output/tsv/chembl_compound-mesh.tsv) ------------------------------ Investigating output/tsv/chembl_compound-mesh.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:15 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-pdb_ccd.tsv is newer than config/chembl_compound-pdb_ccd/config.yaml # File output/tsv/chembl_compound-pdb_ccd.tsv has no timestamp file -# File output/tsv/chembl_compound-pdb_ccd.tsv is created 9.224047296983994 days ago (will be updated when >5 days) -## Update config/chembl_compound-pdb_ccd/config.yaml => output/tsv/chembl_compound-pdb_ccd.tsv -< 2024-12-16T01:36:15 chembl_compound-pdb_ccd -togoid-config config/chembl_compound-pdb_ccd update -# Success: output/tsv/chembl_compound-pdb_ccd.tsv is updated -> 2024-12-16T01:36:15 chembl_compound-pdb_ccd +# File output/tsv/chembl_compound-pdb_ccd.tsv is created 4.776577024118357 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-pdb_ccd.tsv Rule for TSV (output/tsv/chembl_compound-pdb_ccd.tsv) ------------------------------ Investigating output/tsv/chembl_compound-pdb_ccd.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:15 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-pubchem_compound.tsv is newer than config/chembl_compound-pubchem_compound/config.yaml # File output/tsv/chembl_compound-pubchem_compound.tsv has no timestamp file -# File output/tsv/chembl_compound-pubchem_compound.tsv is created 9.224005480637858 days ago (will be updated when >5 days) -## Update config/chembl_compound-pubchem_compound/config.yaml => output/tsv/chembl_compound-pubchem_compound.tsv -< 2024-12-16T01:36:15 chembl_compound-pubchem_compound -togoid-config config/chembl_compound-pubchem_compound update -# Success: output/tsv/chembl_compound-pubchem_compound.tsv is updated -> 2024-12-16T01:36:20 chembl_compound-pubchem_compound +# File output/tsv/chembl_compound-pubchem_compound.tsv is created 4.776524564365891 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-pubchem_compound.tsv Rule for TSV (output/tsv/chembl_compound-pubchem_compound.tsv) ------------------------------ Investigating output/tsv/chembl_compound-pubchem_compound.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:20 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-pubchem_substance if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-pubchem_substance if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-pubchem_substance.tsv is newer than config/chembl_compound-pubchem_substance/config.yaml # File output/tsv/chembl_compound-pubchem_substance.tsv has no timestamp file -# File output/tsv/chembl_compound-pubchem_substance.tsv is created 9.224044386579466 days ago (will be updated when >5 days) -## Update config/chembl_compound-pubchem_substance/config.yaml => output/tsv/chembl_compound-pubchem_substance.tsv -< 2024-12-16T01:36:20 chembl_compound-pubchem_substance -togoid-config config/chembl_compound-pubchem_substance update -# Success: output/tsv/chembl_compound-pubchem_substance.tsv is updated -> 2024-12-16T01:36:22 chembl_compound-pubchem_substance +# File output/tsv/chembl_compound-pubchem_substance.tsv is created 4.776496320931898 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-pubchem_substance.tsv Rule for TSV (output/tsv/chembl_compound-pubchem_substance.tsv) ------------------------------ Investigating output/tsv/chembl_compound-pubchem_substance.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:22 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_compound-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_compound-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_compound-pubmed.tsv is newer than config/chembl_compound-pubmed/config.yaml # File output/tsv/chembl_compound-pubmed.tsv has no timestamp file -# File output/tsv/chembl_compound-pubmed.tsv is created 9.224039270030058 days ago (will be updated when >5 days) -## Update config/chembl_compound-pubmed/config.yaml => output/tsv/chembl_compound-pubmed.tsv -< 2024-12-16T01:36:22 chembl_compound-pubmed -togoid-config config/chembl_compound-pubmed update -# Success: output/tsv/chembl_compound-pubmed.tsv is updated -> 2024-12-16T01:36:26 chembl_compound-pubmed +# File output/tsv/chembl_compound-pubmed.tsv is created 4.776455434879803 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_compound-pubmed.tsv Rule for TSV (output/tsv/chembl_compound-pubmed.tsv) ------------------------------ Investigating output/tsv/chembl_compound-pubmed.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:26 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for chembl_target-ensembl_gene if check_tsv_filesize false or check_config_timestamp true or check_tsv_timestamp true # File output/tsv/chembl_target-ensembl_gene.tsv is older than config/chembl_target-ensembl_gene/config.yaml ## Update config/chembl_target-ensembl_gene/config.yaml => output/tsv/chembl_target-ensembl_gene.tsv -< 2024-12-16T01:36:26 chembl_target-ensembl_gene +< 2024-12-20T20:14:31 chembl_target-ensembl_gene togoid-config config/chembl_target-ensembl_gene update # Error: output/tsv/chembl_target-ensembl_gene.tsv new file size per old 0 / 61845 = 0.0 < 0.5 # Error: Failed to create output/tsv/chembl_target-ensembl_gene.tsv or created file was empty # Failure: output/tsv/chembl_target-ensembl_gene.tsv is not updated -> 2024-12-16T01:36:26 chembl_target-ensembl_gene +> 2024-12-20T20:14:32 chembl_target-ensembl_gene Rule for TSV (output/tsv/chembl_target-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/chembl_target-ensembl_gene.tsv @@ -812,294 +759,270 @@ task needed: true timestamp: 2023-08-25 17:59:01 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-go.tsv is newer than config/chembl_target-go/config.yaml # File output/tsv/chembl_target-go.tsv has no timestamp file -# File output/tsv/chembl_target-go.tsv is created 9.224074673313437 days ago (will be updated when >5 days) -## Update config/chembl_target-go/config.yaml => output/tsv/chembl_target-go.tsv -< 2024-12-16T01:36:26 chembl_target-go -togoid-config config/chembl_target-go update -# Success: output/tsv/chembl_target-go.tsv is updated -> 2024-12-16T01:36:26 chembl_target-go +# File output/tsv/chembl_target-go.tsv is created 4.776450773041818 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-go.tsv Rule for TSV (output/tsv/chembl_target-go.tsv) ------------------------------ Investigating output/tsv/chembl_target-go.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:26 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-interpro.tsv is newer than config/chembl_target-interpro/config.yaml # File output/tsv/chembl_target-interpro.tsv has no timestamp file -# File output/tsv/chembl_target-interpro.tsv is created 9.224074151678067 days ago (will be updated when >5 days) -## Update config/chembl_target-interpro/config.yaml => output/tsv/chembl_target-interpro.tsv -< 2024-12-16T01:36:26 chembl_target-interpro -togoid-config config/chembl_target-interpro update -# Success: output/tsv/chembl_target-interpro.tsv is updated -> 2024-12-16T01:36:27 chembl_target-interpro +# File output/tsv/chembl_target-interpro.tsv is created 4.776445212970567 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-interpro.tsv Rule for TSV (output/tsv/chembl_target-interpro.tsv) ------------------------------ Investigating output/tsv/chembl_target-interpro.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:27 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-pdb.tsv is newer than config/chembl_target-pdb/config.yaml # File output/tsv/chembl_target-pdb.tsv has no timestamp file -# File output/tsv/chembl_target-pdb.tsv is created 9.224074161417661 days ago (will be updated when >5 days) -## Update config/chembl_target-pdb/config.yaml => output/tsv/chembl_target-pdb.tsv -< 2024-12-16T01:36:27 chembl_target-pdb -togoid-config config/chembl_target-pdb update -# Success: output/tsv/chembl_target-pdb.tsv is updated -> 2024-12-16T01:36:27 chembl_target-pdb +# File output/tsv/chembl_target-pdb.tsv is created 4.776440021891597 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-pdb.tsv Rule for TSV (output/tsv/chembl_target-pdb.tsv) ------------------------------ Investigating output/tsv/chembl_target-pdb.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:27 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-pfam.tsv is newer than config/chembl_target-pfam/config.yaml # File output/tsv/chembl_target-pfam.tsv has no timestamp file -# File output/tsv/chembl_target-pfam.tsv is created 9.224074386565903 days ago (will be updated when >5 days) -## Update config/chembl_target-pfam/config.yaml => output/tsv/chembl_target-pfam.tsv -< 2024-12-16T01:36:27 chembl_target-pfam -togoid-config config/chembl_target-pfam update -# Success: output/tsv/chembl_target-pfam.tsv is updated -> 2024-12-16T01:36:28 chembl_target-pfam +# File output/tsv/chembl_target-pfam.tsv is created 4.776435004015162 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-pfam.tsv Rule for TSV (output/tsv/chembl_target-pfam.tsv) ------------------------------ Investigating output/tsv/chembl_target-pfam.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:28 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-reactome_pathway.tsv is newer than config/chembl_target-reactome_pathway/config.yaml # File output/tsv/chembl_target-reactome_pathway.tsv has no timestamp file -# File output/tsv/chembl_target-reactome_pathway.tsv is created 9.224074967438437 days ago (will be updated when >5 days) -## Update config/chembl_target-reactome_pathway/config.yaml => output/tsv/chembl_target-reactome_pathway.tsv -< 2024-12-16T01:36:28 chembl_target-reactome_pathway -togoid-config config/chembl_target-reactome_pathway update -# Success: output/tsv/chembl_target-reactome_pathway.tsv is updated -> 2024-12-16T01:36:28 chembl_target-reactome_pathway +# File output/tsv/chembl_target-reactome_pathway.tsv is created 4.776430009276099 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-reactome_pathway.tsv Rule for TSV (output/tsv/chembl_target-reactome_pathway.tsv) ------------------------------ Investigating output/tsv/chembl_target-reactome_pathway.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:28 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for chembl_target-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for chembl_target-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/chembl_target-uniprot.tsv is newer than config/chembl_target-uniprot/config.yaml # File output/tsv/chembl_target-uniprot.tsv has no timestamp file -# File output/tsv/chembl_target-uniprot.tsv is created 9.224075111457303 days ago (will be updated when >5 days) -## Update config/chembl_target-uniprot/config.yaml => output/tsv/chembl_target-uniprot.tsv -< 2024-12-16T01:36:28 chembl_target-uniprot -togoid-config config/chembl_target-uniprot update -# Success: output/tsv/chembl_target-uniprot.tsv is updated -> 2024-12-16T01:36:29 chembl_target-uniprot +# File output/tsv/chembl_target-uniprot.tsv is created 4.776424910298148 days ago (will be updated when >5 days) +# => Preserving output/tsv/chembl_target-uniprot.tsv Rule for TSV (output/tsv/chembl_target-uniprot.tsv) ------------------------------ Investigating output/tsv/chembl_target-uniprot.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:36:29 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for clinvar-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-dbsnp.tsv is newer than config/clinvar-dbsnp/config.yaml # File output/tsv/clinvar-dbsnp.tsv is older than input/clinvar/download.lock ## Update config/clinvar-dbsnp/config.yaml => output/tsv/clinvar-dbsnp.tsv -< 2024-12-16T01:36:29 clinvar-dbsnp +< 2024-12-20T20:14:32 clinvar-dbsnp togoid-config config/clinvar-dbsnp update # Success: output/tsv/clinvar-dbsnp.tsv is updated -> 2024-12-16T01:37:10 clinvar-dbsnp +> 2024-12-20T20:15:13 clinvar-dbsnp Rule for TSV (output/tsv/clinvar-dbsnp.tsv) ------------------------------ Investigating output/tsv/clinvar-dbsnp.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:37:10 +0900 +timestamp: 2024-12-20 20:15:13 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:37:10 +0900) -latest-prerequisite time: 2024-12-16 01:37:10 +0900 +--prepare:clinvar (2024-12-20 20:15:13 +0900) +latest-prerequisite time: 2024-12-20 20:15:13 +0900 ................................ ### Update TSV for clinvar-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-hgnc.tsv is newer than config/clinvar-hgnc/config.yaml # File output/tsv/clinvar-hgnc.tsv is older than input/clinvar/download.lock ## Update config/clinvar-hgnc/config.yaml => output/tsv/clinvar-hgnc.tsv -< 2024-12-16T01:37:10 clinvar-hgnc +< 2024-12-20T20:15:13 clinvar-hgnc togoid-config config/clinvar-hgnc update # Success: output/tsv/clinvar-hgnc.tsv is updated -> 2024-12-16T01:38:03 clinvar-hgnc +> 2024-12-20T20:16:08 clinvar-hgnc Rule for TSV (output/tsv/clinvar-hgnc.tsv) ------------------------------ Investigating output/tsv/clinvar-hgnc.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:38:03 +0900 +timestamp: 2024-12-20 20:16:08 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:38:03 +0900) -latest-prerequisite time: 2024-12-16 01:38:03 +0900 +--prepare:clinvar (2024-12-20 20:16:08 +0900) +latest-prerequisite time: 2024-12-20 20:16:08 +0900 ................................ ### Update TSV for clinvar-medgen if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-medgen.tsv is newer than config/clinvar-medgen/config.yaml # File output/tsv/clinvar-medgen.tsv is older than input/clinvar/download.lock ## Update config/clinvar-medgen/config.yaml => output/tsv/clinvar-medgen.tsv -< 2024-12-16T01:38:03 clinvar-medgen +< 2024-12-20T20:16:08 clinvar-medgen togoid-config config/clinvar-medgen update # Success: output/tsv/clinvar-medgen.tsv is updated -> 2024-12-16T01:39:39 clinvar-medgen +> 2024-12-20T20:17:45 clinvar-medgen Rule for TSV (output/tsv/clinvar-medgen.tsv) ------------------------------ Investigating output/tsv/clinvar-medgen.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:39:39 +0900 +timestamp: 2024-12-20 20:17:45 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:39:39 +0900) -latest-prerequisite time: 2024-12-16 01:39:39 +0900 +--prepare:clinvar (2024-12-20 20:17:45 +0900) +latest-prerequisite time: 2024-12-20 20:17:45 +0900 ................................ ### Update TSV for clinvar-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-mondo.tsv is newer than config/clinvar-mondo/config.yaml # File output/tsv/clinvar-mondo.tsv is older than input/clinvar/download.lock ## Update config/clinvar-mondo/config.yaml => output/tsv/clinvar-mondo.tsv -< 2024-12-16T01:39:39 clinvar-mondo +< 2024-12-20T20:17:45 clinvar-mondo togoid-config config/clinvar-mondo update # Success: output/tsv/clinvar-mondo.tsv is updated -> 2024-12-16T01:41:09 clinvar-mondo +> 2024-12-20T20:19:17 clinvar-mondo Rule for TSV (output/tsv/clinvar-mondo.tsv) ------------------------------ Investigating output/tsv/clinvar-mondo.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:41:09 +0900 +timestamp: 2024-12-20 20:19:17 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:41:09 +0900) -latest-prerequisite time: 2024-12-16 01:41:09 +0900 +--prepare:clinvar (2024-12-20 20:19:17 +0900) +latest-prerequisite time: 2024-12-20 20:19:17 +0900 ................................ ### Update TSV for clinvar-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-ncbigene.tsv is newer than config/clinvar-ncbigene/config.yaml # File output/tsv/clinvar-ncbigene.tsv is older than input/clinvar/download.lock ## Update config/clinvar-ncbigene/config.yaml => output/tsv/clinvar-ncbigene.tsv -< 2024-12-16T01:41:09 clinvar-ncbigene +< 2024-12-20T20:19:17 clinvar-ncbigene togoid-config config/clinvar-ncbigene update # Success: output/tsv/clinvar-ncbigene.tsv is updated -> 2024-12-16T01:42:01 clinvar-ncbigene +> 2024-12-20T20:20:11 clinvar-ncbigene Rule for TSV (output/tsv/clinvar-ncbigene.tsv) ------------------------------ Investigating output/tsv/clinvar-ncbigene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:42:01 +0900 +timestamp: 2024-12-20 20:20:11 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:42:01 +0900) -latest-prerequisite time: 2024-12-16 01:42:01 +0900 +--prepare:clinvar (2024-12-20 20:20:11 +0900) +latest-prerequisite time: 2024-12-20 20:20:11 +0900 ................................ ### Update TSV for clinvar-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-omim_phenotype.tsv is newer than config/clinvar-omim_phenotype/config.yaml # File output/tsv/clinvar-omim_phenotype.tsv is older than input/clinvar/download.lock ## Update config/clinvar-omim_phenotype/config.yaml => output/tsv/clinvar-omim_phenotype.tsv -< 2024-12-16T01:42:01 clinvar-omim_phenotype +< 2024-12-20T20:20:11 clinvar-omim_phenotype togoid-config config/clinvar-omim_phenotype update # Success: output/tsv/clinvar-omim_phenotype.tsv is updated -> 2024-12-16T01:43:31 clinvar-omim_phenotype +> 2024-12-20T20:21:42 clinvar-omim_phenotype Rule for TSV (output/tsv/clinvar-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/clinvar-omim_phenotype.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:43:31 +0900 +timestamp: 2024-12-20 20:21:42 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:43:31 +0900) -latest-prerequisite time: 2024-12-16 01:43:31 +0900 +--prepare:clinvar (2024-12-20 20:21:42 +0900) +latest-prerequisite time: 2024-12-20 20:21:42 +0900 ................................ ### Update TSV for clinvar-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-orphanet_phenotype.tsv is newer than config/clinvar-orphanet_phenotype/config.yaml # File output/tsv/clinvar-orphanet_phenotype.tsv is older than input/clinvar/download.lock ## Update config/clinvar-orphanet_phenotype/config.yaml => output/tsv/clinvar-orphanet_phenotype.tsv -< 2024-12-16T01:43:31 clinvar-orphanet_phenotype +< 2024-12-20T20:21:42 clinvar-orphanet_phenotype togoid-config config/clinvar-orphanet_phenotype update # Success: output/tsv/clinvar-orphanet_phenotype.tsv is updated -> 2024-12-16T01:45:01 clinvar-orphanet_phenotype +> 2024-12-20T20:23:15 clinvar-orphanet_phenotype Rule for TSV (output/tsv/clinvar-orphanet_phenotype.tsv) ------------------------------ Investigating output/tsv/clinvar-orphanet_phenotype.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:45:01 +0900 +timestamp: 2024-12-20 20:23:15 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:45:01 +0900) -latest-prerequisite time: 2024-12-16 01:45:01 +0900 +--prepare:clinvar (2024-12-20 20:23:15 +0900) +latest-prerequisite time: 2024-12-20 20:23:15 +0900 ................................ ### Update TSV for clinvar-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/clinvar-uniprot.tsv is newer than config/clinvar-uniprot/config.yaml # File output/tsv/clinvar-uniprot.tsv is older than input/clinvar/download.lock ## Update config/clinvar-uniprot/config.yaml => output/tsv/clinvar-uniprot.tsv -< 2024-12-16T01:45:01 clinvar-uniprot +< 2024-12-20T20:23:15 clinvar-uniprot togoid-config config/clinvar-uniprot update # Success: output/tsv/clinvar-uniprot.tsv is updated -> 2024-12-16T01:45:51 clinvar-uniprot +> 2024-12-20T20:24:05 clinvar-uniprot Rule for TSV (output/tsv/clinvar-uniprot.tsv) ------------------------------ Investigating output/tsv/clinvar-uniprot.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 01:45:51 +0900 +timestamp: 2024-12-20 20:24:05 +0900 pre-requisites: --output/tsv/ () ---prepare:clinvar (2024-12-16 01:45:51 +0900) -latest-prerequisite time: 2024-12-16 01:45:51 +0900 +--prepare:clinvar (2024-12-20 20:24:05 +0900) +latest-prerequisite time: 2024-12-20 20:24:05 +0900 ................................ ### Update TSV for cog-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1114,8 +1037,8 @@ task needed: true timestamp: 2023-07-28 17:55:29 +0900 pre-requisites: --output/tsv/ () ---prepare:cog (2024-12-16 01:45:51 +0900) -latest-prerequisite time: 2024-12-16 01:45:51 +0900 +--prepare:cog (2024-12-20 20:24:05 +0900) +latest-prerequisite time: 2024-12-20 20:24:05 +0900 ................................ ### Update TSV for cog-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1130,82 +1053,66 @@ task needed: true timestamp: 2023-07-28 17:55:40 +0900 pre-requisites: --output/tsv/ () ---prepare:cog (2024-12-16 01:45:51 +0900) -latest-prerequisite time: 2024-12-16 01:45:51 +0900 +--prepare:cog (2024-12-20 20:24:05 +0900) +latest-prerequisite time: 2024-12-20 20:24:05 +0900 ................................ -### Update TSV for doid-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for doid-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/doid-mesh.tsv is newer than config/doid-mesh/config.yaml # File output/tsv/doid-mesh.tsv has no timestamp file -# File output/tsv/doid-mesh.tsv is created 9.224076492894953 days ago (will be updated when >5 days) -## Update config/doid-mesh/config.yaml => output/tsv/doid-mesh.tsv -< 2024-12-16T01:45:51 doid-mesh -togoid-config config/doid-mesh update -# Success: output/tsv/doid-mesh.tsv is updated -> 2024-12-16T01:45:52 doid-mesh +# File output/tsv/doid-mesh.tsv is created 4.776535647042269 days ago (will be updated when >5 days) +# => Preserving output/tsv/doid-mesh.tsv Rule for TSV (output/tsv/doid-mesh.tsv) ------------------------------ Investigating output/tsv/doid-mesh.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:45:52 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for doid-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for doid-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/doid-ncit_disease.tsv is newer than config/doid-ncit_disease/config.yaml # File output/tsv/doid-ncit_disease.tsv has no timestamp file -# File output/tsv/doid-ncit_disease.tsv is created 9.224076087960231 days ago (will be updated when >5 days) -## Update config/doid-ncit_disease/config.yaml => output/tsv/doid-ncit_disease.tsv -< 2024-12-16T01:45:52 doid-ncit_disease -togoid-config config/doid-ncit_disease update -# Success: output/tsv/doid-ncit_disease.tsv is updated -> 2024-12-16T01:45:52 doid-ncit_disease +# File output/tsv/doid-ncit_disease.tsv is created 4.776530664124479 days ago (will be updated when >5 days) +# => Preserving output/tsv/doid-ncit_disease.tsv Rule for TSV (output/tsv/doid-ncit_disease.tsv) ------------------------------ Investigating output/tsv/doid-ncit_disease.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:45:52 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for doid-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for doid-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/doid-omim_phenotype.tsv is newer than config/doid-omim_phenotype/config.yaml # File output/tsv/doid-omim_phenotype.tsv has no timestamp file -# File output/tsv/doid-omim_phenotype.tsv is created 9.224075732428183 days ago (will be updated when >5 days) -## Update config/doid-omim_phenotype/config.yaml => output/tsv/doid-omim_phenotype.tsv -< 2024-12-16T01:45:52 doid-omim_phenotype -togoid-config config/doid-omim_phenotype update -# Success: output/tsv/doid-omim_phenotype.tsv is updated -> 2024-12-16T01:45:53 doid-omim_phenotype +# File output/tsv/doid-omim_phenotype.tsv is created 4.776525982001216 days ago (will be updated when >5 days) +# => Preserving output/tsv/doid-omim_phenotype.tsv Rule for TSV (output/tsv/doid-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/doid-omim_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 01:45:53 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for ensembl_gene-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for ensembl_gene-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/ensembl_gene-affy_probeset.tsv is newer than config/ensembl_gene-affy_probeset/config.yaml # File output/tsv/ensembl_gene-affy_probeset.tsv has no timestamp file -# File output/tsv/ensembl_gene-affy_probeset.tsv is created 9.223513251984155 days ago (will be updated when >5 days) -## Update config/ensembl_gene-affy_probeset/config.yaml => output/tsv/ensembl_gene-affy_probeset.tsv -< 2024-12-16T01:45:53 ensembl_gene-affy_probeset -togoid-config config/ensembl_gene-affy_probeset update -# Success: output/tsv/ensembl_gene-affy_probeset.tsv is updated -> 2024-12-16T01:46:57 ensembl_gene-affy_probeset +# File output/tsv/ensembl_gene-affy_probeset.tsv is created 4.775784072709711 days ago (will be updated when >5 days) +# => Preserving output/tsv/ensembl_gene-affy_probeset.tsv Rule for TSV (output/tsv/ensembl_gene-affy_probeset.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-affy_probeset.tsv @@ -1214,65 +1121,57 @@ task needed: true timestamp: 2024-12-16 01:46:57 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:57 +0900) -latest-prerequisite time: 2024-12-16 01:46:57 +0900 +--prepare:ensembl (2024-12-20 20:24:05 +0900) +latest-prerequisite time: 2024-12-20 20:24:05 +0900 ................................ ### Update TSV for ensembl_gene-ensembl_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_gene-ensembl_protein.tsv is newer than config/ensembl_gene-ensembl_protein/config.yaml # File output/tsv/ensembl_gene-ensembl_protein.tsv has no timestamp file -# File output/tsv/ensembl_gene-ensembl_protein.tsv is created 9.22300119364082 days ago (will be updated when >5 days) +# File output/tsv/ensembl_gene-ensembl_protein.tsv is created 13.998785199981784 days ago (will be updated when >5 days) ## Update config/ensembl_gene-ensembl_protein/config.yaml => output/tsv/ensembl_gene-ensembl_protein.tsv -< 2024-12-16T01:46:57 ensembl_gene-ensembl_protein +< 2024-12-20T20:24:05 ensembl_gene-ensembl_protein togoid-config config/ensembl_gene-ensembl_protein update -# Error: output/tsv/ensembl_gene-ensembl_protein.tsv new file size per old 0 / 493740466 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ensembl_protein.tsv or created file was empty -# Failure: output/tsv/ensembl_gene-ensembl_protein.tsv is not updated -> 2024-12-16T01:46:57 ensembl_gene-ensembl_protein +# Success: output/tsv/ensembl_gene-ensembl_protein.tsv is updated +> 2024-12-20T20:25:56 ensembl_gene-ensembl_protein Rule for TSV (output/tsv/ensembl_gene-ensembl_protein.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-ensembl_protein.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:25:50 +0900 +timestamp: 2024-12-20 20:25:56 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:57 +0900) -latest-prerequisite time: 2024-12-16 01:46:57 +0900 +--prepare:ensembl (2024-12-20 20:25:56 +0900) +latest-prerequisite time: 2024-12-20 20:25:56 +0900 ................................ ### Update TSV for ensembl_gene-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_gene-ensembl_transcript.tsv is newer than config/ensembl_gene-ensembl_transcript/config.yaml # File output/tsv/ensembl_gene-ensembl_transcript.tsv has no timestamp file -# File output/tsv/ensembl_gene-ensembl_transcript.tsv is created 9.221533021723934 days ago (will be updated when >5 days) +# File output/tsv/ensembl_gene-ensembl_transcript.tsv is created 13.998603338460429 days ago (will be updated when >5 days) ## Update config/ensembl_gene-ensembl_transcript/config.yaml => output/tsv/ensembl_gene-ensembl_transcript.tsv -< 2024-12-16T01:46:57 ensembl_gene-ensembl_transcript +< 2024-12-20T20:25:56 ensembl_gene-ensembl_transcript togoid-config config/ensembl_gene-ensembl_transcript update -# Error: output/tsv/ensembl_gene-ensembl_transcript.tsv new file size per old 0 / 606499011 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ensembl_transcript.tsv or created file was empty -# Failure: output/tsv/ensembl_gene-ensembl_transcript.tsv is not updated -> 2024-12-16T01:46:57 ensembl_gene-ensembl_transcript +# Success: output/tsv/ensembl_gene-ensembl_transcript.tsv is updated +> 2024-12-20T20:28:00 ensembl_gene-ensembl_transcript Rule for TSV (output/tsv/ensembl_gene-ensembl_transcript.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-ensembl_transcript.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:27:57 +0900 +timestamp: 2024-12-20 20:28:00 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:57 +0900) -latest-prerequisite time: 2024-12-16 01:46:57 +0900 +--prepare:ensembl (2024-12-20 20:28:00 +0900) +latest-prerequisite time: 2024-12-20 20:28:00 +0900 ................................ -### Update TSV for ensembl_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for ensembl_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/ensembl_gene-hgnc.tsv is newer than config/ensembl_gene-hgnc/config.yaml # File output/tsv/ensembl_gene-hgnc.tsv has no timestamp file -# File output/tsv/ensembl_gene-hgnc.tsv is created 9.221530478998067 days ago (will be updated when >5 days) -## Update config/ensembl_gene-hgnc/config.yaml => output/tsv/ensembl_gene-hgnc.tsv -< 2024-12-16T01:46:57 ensembl_gene-hgnc -togoid-config config/ensembl_gene-hgnc update -# Success: output/tsv/ensembl_gene-hgnc.tsv is updated -> 2024-12-16T01:46:58 ensembl_gene-hgnc +# File output/tsv/ensembl_gene-hgnc.tsv is created 4.778496467369919 days ago (will be updated when >5 days) +# => Preserving output/tsv/ensembl_gene-hgnc.tsv Rule for TSV (output/tsv/ensembl_gene-hgnc.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-hgnc.tsv @@ -1281,88 +1180,197 @@ task needed: true timestamp: 2024-12-16 01:46:58 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:58 +0900) -latest-prerequisite time: 2024-12-16 01:46:58 +0900 +--prepare:ensembl (2024-12-20 20:28:00 +0900) +latest-prerequisite time: 2024-12-20 20:28:00 +0900 ................................ ### Update TSV for ensembl_gene-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_gene-ncbigene.tsv is newer than config/ensembl_gene-ncbigene/config.yaml # File output/tsv/ensembl_gene-ncbigene.tsv has no timestamp file -# File output/tsv/ensembl_gene-ncbigene.tsv is created 9.220169899221956 days ago (will be updated when >5 days) +# File output/tsv/ensembl_gene-ncbigene.tsv is created 13.99866625925191 days ago (will be updated when >5 days) ## Update config/ensembl_gene-ncbigene/config.yaml => output/tsv/ensembl_gene-ncbigene.tsv -< 2024-12-16T01:46:58 ensembl_gene-ncbigene +< 2024-12-20T20:28:00 ensembl_gene-ncbigene togoid-config config/ensembl_gene-ncbigene update -# Error: output/tsv/ensembl_gene-ncbigene.tsv new file size per old 0 / 425488063 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-ncbigene.tsv or created file was empty -# Failure: output/tsv/ensembl_gene-ncbigene.tsv is not updated -> 2024-12-16T01:46:58 ensembl_gene-ncbigene +Warning: Failed to retrieve taxon:8840 in loop_count:1 +Warning: Failed to retrieve taxon:9771 in loop_count:1 +Warning: Failed to retrieve taxon:30521 in loop_count:1 +Warning: Failed to retrieve taxon:61819 in loop_count:1 +Warning: Failed to retrieve taxon:8823 in loop_count:1 +Warning: Failed to retrieve taxon:224669 in loop_count:1 +Warning: Failed to retrieve taxon:51154 in loop_count:1 +Warning: Failed to retrieve taxon:91951 in loop_count:1 +Warning: Failed to retrieve taxon:37548 in loop_count:1 +Warning: Failed to retrieve taxon:84702 in loop_count:1 +Warning: Failed to retrieve taxon:106734 in loop_count:1 +Warning: Failed to retrieve taxon:8103 in loop_count:1 +Warning: Failed to retrieve taxon:100819 in loop_count:1 +Warning: Failed to retrieve taxon:75864 in loop_count:1 +Warning: Failed to retrieve taxon:211598 in loop_count:1 +Warning: Failed to retrieve taxon:161767 in loop_count:1 +Warning: Failed to retrieve taxon:132585 in loop_count:1 +Warning: Failed to retrieve taxon:8845 in loop_count:1 +Warning: Failed to retrieve taxon:425635 in loop_count:1 +Warning: Failed to retrieve taxon:13489 in loop_count:1 +Warning: Failed to retrieve taxon:241587 in loop_count:1 +Warning: Failed to retrieve taxon:30461 in loop_count:1 +Warning: Failed to retrieve taxon:1240228 in loop_count:1 +Warning: Failed to retrieve taxon:8824 in loop_count:1 +Warning: Failed to retrieve taxon:8475 in loop_count:1 +Warning: Failed to retrieve taxon:9358 in loop_count:1 +Warning: Failed to retrieve taxon:7764 in loop_count:1 +Warning: Failed to retrieve taxon:2593467 in loop_count:1 +Warning: Failed to retrieve taxon:68415 in loop_count:1 +Warning: Failed to retrieve taxon:9315 in loop_count:1 +Warning: Failed to retrieve taxon:123683 in loop_count:1 +Warning: Failed to retrieve taxon:9089 in loop_count:1 +Warning: Failed to retrieve taxon:40217 in loop_count:1 +Warning: Failed to retrieve taxon:8630 in loop_count:1 +Warning: Failed to retrieve taxon:445787 in loop_count:1 +Warning: Failed to retrieve taxon:10096 in loop_count:1 +Warning: Failed to retrieve taxon:62062 in loop_count:1 +Warning: Failed to retrieve taxon:44316 in loop_count:1 +Warning: Failed to retrieve taxon:38772 in loop_count:1 +Warning: Failed to retrieve taxon:47969 in loop_count:1 +Warning: Failed to retrieve taxon:183150 in loop_count:1 +Warning: Failed to retrieve taxon:9054 in loop_count:1 +Warning: Failed to retrieve taxon:94237 in loop_count:1 +Warning: Failed to retrieve taxon:10103 in loop_count:1 +Warning: Failed to retrieve taxon:35670 in loop_count:1 +Warning: Failed to retrieve taxon:47308 in loop_count:1 +Warning: Failed to retrieve taxon:257818 in loop_count:1 +Warning: Failed to retrieve taxon:74533 in loop_count:1 +Warning: Failed to retrieve taxon:367368 in loop_count:1 +Warning: Failed to retrieve taxon:1328070 in loop_count:1 +Warning: Failed to retrieve taxon:8508 in loop_count:1 +Warning: Failed to retrieve taxon:311401 in loop_count:1 +Warning: Failed to retrieve taxon:9049 in loop_count:1 +Warning: Failed to retrieve taxon:9643 in loop_count:1 +Warning: Failed to retrieve taxon:59479 in loop_count:1 +Warning: Failed to retrieve taxon:1220523 in loop_count:1 +Warning: Failed to retrieve taxon:96440 in loop_count:1 +Warning: Failed to retrieve taxon:55149 in loop_count:1 +Warning: Failed to retrieve taxon:441215 in loop_count:1 +Warning: Failed to retrieve taxon:61221 in loop_count:1 +Warning: Failed to retrieve taxon:99837 in loop_count:1 +Warning: Failed to retrieve taxon:37032 in loop_count:1 +Warning: Failed to retrieve taxon:181631 in loop_count:1 +# Success: output/tsv/ensembl_gene-ncbigene.tsv is updated +> 2024-12-20T20:29:58 ensembl_gene-ncbigene Rule for TSV (output/tsv/ensembl_gene-ncbigene.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-ncbigene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:29:55 +0900 +timestamp: 2024-12-20 20:29:58 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:58 +0900) -latest-prerequisite time: 2024-12-16 01:46:58 +0900 +--prepare:ensembl (2024-12-20 20:29:58 +0900) +latest-prerequisite time: 2024-12-20 20:29:58 +0900 ................................ ### Update TSV for ensembl_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_gene-uniprot.tsv is newer than config/ensembl_gene-uniprot/config.yaml # File output/tsv/ensembl_gene-uniprot.tsv has no timestamp file -# File output/tsv/ensembl_gene-uniprot.tsv is created 9.219176207811111 days ago (will be updated when >5 days) +# File output/tsv/ensembl_gene-uniprot.tsv is created 13.999034877016586 days ago (will be updated when >5 days) ## Update config/ensembl_gene-uniprot/config.yaml => output/tsv/ensembl_gene-uniprot.tsv -< 2024-12-16T01:46:58 ensembl_gene-uniprot +< 2024-12-20T20:29:58 ensembl_gene-uniprot togoid-config config/ensembl_gene-uniprot update -# Error: output/tsv/ensembl_gene-uniprot.tsv new file size per old 0 / 159598297 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_gene-uniprot.tsv or created file was empty -# Failure: output/tsv/ensembl_gene-uniprot.tsv is not updated -> 2024-12-16T01:46:58 ensembl_gene-uniprot +Warning: Failed to retrieve taxon:9771 in loop_count:1 +Warning: Failed to retrieve taxon:8823 in loop_count:1 +Warning: Failed to retrieve taxon:224669 in loop_count:1 +Warning: Failed to retrieve taxon:51154 in loop_count:1 +Warning: Failed to retrieve taxon:91951 in loop_count:1 +Warning: Failed to retrieve taxon:84702 in loop_count:1 +Warning: Failed to retrieve taxon:106734 in loop_count:1 +Warning: Failed to retrieve taxon:156563 in loop_count:1 +Warning: Failed to retrieve taxon:308060 in loop_count:1 +Warning: Failed to retrieve taxon:100819 in loop_count:1 +Warning: Failed to retrieve taxon:223781 in loop_count:1 +Warning: Failed to retrieve taxon:425635 in loop_count:1 +Warning: Failed to retrieve taxon:241587 in loop_count:1 +Warning: Failed to retrieve taxon:198806 in loop_count:1 +Warning: Failed to retrieve taxon:194338 in loop_count:1 +Warning: Failed to retrieve taxon:158456 in loop_count:1 +Warning: Failed to retrieve taxon:30461 in loop_count:1 +Warning: Failed to retrieve taxon:1240228 in loop_count:1 +Warning: Failed to retrieve taxon:8824 in loop_count:1 +Warning: Failed to retrieve taxon:286419 in loop_count:1 +Warning: Failed to retrieve taxon:2593467 in loop_count:1 +Warning: Failed to retrieve taxon:9994 in loop_count:1 +Warning: Failed to retrieve taxon:9089 in loop_count:1 +Warning: Failed to retrieve taxon:299321 in loop_count:1 +Warning: Failed to retrieve taxon:173247 in loop_count:1 +Warning: Failed to retrieve taxon:27687 in loop_count:1 +Warning: Failed to retrieve taxon:40217 in loop_count:1 +Warning: Failed to retrieve taxon:8630 in loop_count:1 +Warning: Failed to retrieve taxon:445787 in loop_count:1 +Warning: Failed to retrieve taxon:441366 in loop_count:1 +Warning: Failed to retrieve taxon:1825980 in loop_count:1 +Warning: Failed to retrieve taxon:321398 in loop_count:1 +Warning: Failed to retrieve taxon:35670 in loop_count:1 +Warning: Failed to retrieve taxon:30464 in loop_count:1 +Warning: Failed to retrieve taxon:586833 in loop_count:1 +Warning: Failed to retrieve taxon:47308 in loop_count:1 +Warning: Failed to retrieve taxon:257818 in loop_count:1 +Warning: Failed to retrieve taxon:591936 in loop_count:1 +Warning: Failed to retrieve taxon:64176 in loop_count:1 +Warning: Failed to retrieve taxon:1328070 in loop_count:1 +Warning: Failed to retrieve taxon:375764 in loop_count:1 +Warning: Failed to retrieve taxon:2489341 in loop_count:1 +Warning: Failed to retrieve taxon:311401 in loop_count:1 +Warning: Failed to retrieve taxon:2587831 in loop_count:1 +Warning: Failed to retrieve taxon:210632 in loop_count:1 +Warning: Failed to retrieve taxon:103695 in loop_count:1 +Warning: Failed to retrieve taxon:42100 in loop_count:1 +Warning: Failed to retrieve taxon:181472 in loop_count:1 +Warning: Failed to retrieve taxon:1220523 in loop_count:1 +Warning: Failed to retrieve taxon:96440 in loop_count:1 +Warning: Failed to retrieve taxon:55149 in loop_count:1 +Warning: Failed to retrieve taxon:441215 in loop_count:1 +Warning: Failed to retrieve taxon:99837 in loop_count:1 +Warning: Failed to retrieve taxon:37032 in loop_count:1 +Warning: Failed to retrieve taxon:181631 in loop_count:1 +Warning: Failed to retrieve taxon:9999 in loop_count:1 +# Success: output/tsv/ensembl_gene-uniprot.tsv is updated +> 2024-12-20T20:31:23 ensembl_gene-uniprot Rule for TSV (output/tsv/ensembl_gene-uniprot.tsv) ------------------------------ Investigating output/tsv/ensembl_gene-uniprot.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:31:21 +0900 +timestamp: 2024-12-20 20:31:23 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:58 +0900) -latest-prerequisite time: 2024-12-16 01:46:58 +0900 +--prepare:ensembl (2024-12-20 20:31:23 +0900) +latest-prerequisite time: 2024-12-20 20:31:23 +0900 ................................ ### Update TSV for ensembl_protein-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_protein-ensembl_transcript.tsv is newer than config/ensembl_protein-ensembl_transcript/config.yaml # File output/tsv/ensembl_protein-ensembl_transcript.tsv has no timestamp file -# File output/tsv/ensembl_protein-ensembl_transcript.tsv is created 9.217785663917546 days ago (will be updated when >5 days) +# File output/tsv/ensembl_protein-ensembl_transcript.tsv is created 13.998627880603184 days ago (will be updated when >5 days) ## Update config/ensembl_protein-ensembl_transcript/config.yaml => output/tsv/ensembl_protein-ensembl_transcript.tsv -< 2024-12-16T01:46:58 ensembl_protein-ensembl_transcript +< 2024-12-20T20:31:23 ensembl_protein-ensembl_transcript togoid-config config/ensembl_protein-ensembl_transcript update -# Error: output/tsv/ensembl_protein-ensembl_transcript.tsv new file size per old 0 / 493651516 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_protein-ensembl_transcript.tsv or created file was empty -# Failure: output/tsv/ensembl_protein-ensembl_transcript.tsv is not updated -> 2024-12-16T01:46:59 ensembl_protein-ensembl_transcript +# Success: output/tsv/ensembl_protein-ensembl_transcript.tsv is updated +> 2024-12-20T20:33:18 ensembl_protein-ensembl_transcript Rule for TSV (output/tsv/ensembl_protein-ensembl_transcript.tsv) ------------------------------ Investigating output/tsv/ensembl_protein-ensembl_transcript.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:33:22 +0900 +timestamp: 2024-12-20 20:33:18 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:46:59 +0900) -latest-prerequisite time: 2024-12-16 01:46:59 +0900 +--prepare:ensembl (2024-12-20 20:33:18 +0900) +latest-prerequisite time: 2024-12-20 20:33:18 +0900 ................................ -### Update TSV for ensembl_transcript-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for ensembl_transcript-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/ensembl_transcript-affy_probeset.tsv is newer than config/ensembl_transcript-affy_probeset/config.yaml # File output/tsv/ensembl_transcript-affy_probeset.tsv has no timestamp file -# File output/tsv/ensembl_transcript-affy_probeset.tsv is created 9.217177651396412 days ago (will be updated when >5 days) -## Update config/ensembl_transcript-affy_probeset/config.yaml => output/tsv/ensembl_transcript-affy_probeset.tsv -< 2024-12-16T01:46:59 ensembl_transcript-affy_probeset -togoid-config config/ensembl_transcript-affy_probeset update -# Success: output/tsv/ensembl_transcript-affy_probeset.tsv is updated -> 2024-12-16T01:48:04 ensembl_transcript-affy_probeset +# File output/tsv/ensembl_transcript-affy_probeset.tsv is created 4.781415301968055 days ago (will be updated when >5 days) +# => Preserving output/tsv/ensembl_transcript-affy_probeset.tsv Rule for TSV (output/tsv/ensembl_transcript-affy_probeset.tsv) ------------------------------ Investigating output/tsv/ensembl_transcript-affy_probeset.tsv @@ -1371,42 +1379,36 @@ task needed: true timestamp: 2024-12-16 01:48:04 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:48:04 +0900) -latest-prerequisite time: 2024-12-16 01:48:04 +0900 +--prepare:ensembl (2024-12-20 20:33:18 +0900) +latest-prerequisite time: 2024-12-20 20:33:18 +0900 ................................ ### Update TSV for ensembl_transcript-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_transcript-go.tsv is newer than config/ensembl_transcript-go/config.yaml # File output/tsv/ensembl_transcript-go.tsv has no timestamp file -# File output/tsv/ensembl_transcript-go.tsv is created 9.21511766733595 days ago (will be updated when >5 days) +# File output/tsv/ensembl_transcript-go.tsv is created 13.996532846736075 days ago (will be updated when >5 days) ## Update config/ensembl_transcript-go/config.yaml => output/tsv/ensembl_transcript-go.tsv -< 2024-12-16T01:48:04 ensembl_transcript-go +< 2024-12-20T20:33:18 ensembl_transcript-go togoid-config config/ensembl_transcript-go update -# Error: output/tsv/ensembl_transcript-go.tsv new file size per old 0 / 1491765002 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_transcript-go.tsv or created file was empty -# Failure: output/tsv/ensembl_transcript-go.tsv is not updated -> 2024-12-16T01:48:04 ensembl_transcript-go +# Success: output/tsv/ensembl_transcript-go.tsv is updated +> 2024-12-20T20:37:29 ensembl_transcript-go Rule for TSV (output/tsv/ensembl_transcript-go.tsv) ------------------------------ Investigating output/tsv/ensembl_transcript-go.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:38:18 +0900 +timestamp: 2024-12-20 20:37:29 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:48:04 +0900) -latest-prerequisite time: 2024-12-16 01:48:04 +0900 +--prepare:ensembl (2024-12-20 20:37:29 +0900) +latest-prerequisite time: 2024-12-20 20:37:29 +0900 ................................ -### Update TSV for ensembl_transcript-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for ensembl_transcript-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/ensembl_transcript-hgnc.tsv is newer than config/ensembl_transcript-hgnc/config.yaml # File output/tsv/ensembl_transcript-hgnc.tsv has no timestamp file -# File output/tsv/ensembl_transcript-hgnc.tsv is created 9.21511068299728 days ago (will be updated when >5 days) -## Update config/ensembl_transcript-hgnc/config.yaml => output/tsv/ensembl_transcript-hgnc.tsv -< 2024-12-16T01:48:04 ensembl_transcript-hgnc -togoid-config config/ensembl_transcript-hgnc update -# Success: output/tsv/ensembl_transcript-hgnc.tsv is updated -> 2024-12-16T01:48:05 ensembl_transcript-hgnc +# File output/tsv/ensembl_transcript-hgnc.tsv is created 4.784302660551678 days ago (will be updated when >5 days) +# => Preserving output/tsv/ensembl_transcript-hgnc.tsv Rule for TSV (output/tsv/ensembl_transcript-hgnc.tsv) ------------------------------ Investigating output/tsv/ensembl_transcript-hgnc.tsv @@ -1415,93 +1417,153 @@ task needed: true timestamp: 2024-12-16 01:48:05 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:48:05 +0900) -latest-prerequisite time: 2024-12-16 01:48:05 +0900 +--prepare:ensembl (2024-12-20 20:37:29 +0900) +latest-prerequisite time: 2024-12-20 20:37:29 +0900 ................................ ### Update TSV for ensembl_transcript-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ensembl_transcript-refseq_rna.tsv is newer than config/ensembl_transcript-refseq_rna/config.yaml # File output/tsv/ensembl_transcript-refseq_rna.tsv has no timestamp file -# File output/tsv/ensembl_transcript-refseq_rna.tsv is created 9.212762598192556 days ago (will be updated when >5 days) +# File output/tsv/ensembl_transcript-refseq_rna.tsv is created 13.997065152819317 days ago (will be updated when >5 days) ## Update config/ensembl_transcript-refseq_rna/config.yaml => output/tsv/ensembl_transcript-refseq_rna.tsv -< 2024-12-16T01:48:05 ensembl_transcript-refseq_rna +< 2024-12-20T20:37:29 ensembl_transcript-refseq_rna togoid-config config/ensembl_transcript-refseq_rna update -# Error: output/tsv/ensembl_transcript-refseq_rna.tsv new file size per old 0 / 1283309099 = 0.0 < 0.5 -# Error: Failed to create output/tsv/ensembl_transcript-refseq_rna.tsv or created file was empty -# Failure: output/tsv/ensembl_transcript-refseq_rna.tsv is not updated -> 2024-12-16T01:48:05 ensembl_transcript-refseq_rna +Warning: Failed to retrieve taxon:8840 in loop_count:1 +Warning: Failed to retrieve taxon:9771 in loop_count:1 +Warning: Failed to retrieve taxon:30521 in loop_count:1 +Warning: Failed to retrieve taxon:61819 in loop_count:1 +Warning: Failed to retrieve taxon:8823 in loop_count:1 +Warning: Failed to retrieve taxon:224669 in loop_count:1 +Warning: Failed to retrieve taxon:51154 in loop_count:1 +Warning: Failed to retrieve taxon:91951 in loop_count:1 +Warning: Failed to retrieve taxon:37548 in loop_count:1 +Warning: Failed to retrieve taxon:84702 in loop_count:1 +Warning: Failed to retrieve taxon:106734 in loop_count:1 +Warning: Failed to retrieve taxon:8103 in loop_count:1 +Warning: Failed to retrieve taxon:630221 in loop_count:1 +Warning: Failed to retrieve taxon:100819 in loop_count:1 +Warning: Failed to retrieve taxon:75864 in loop_count:1 +Warning: Failed to retrieve taxon:211598 in loop_count:1 +Warning: Failed to retrieve taxon:161767 in loop_count:1 +Warning: Failed to retrieve taxon:132585 in loop_count:1 +Warning: Failed to retrieve taxon:8845 in loop_count:1 +Warning: Failed to retrieve taxon:425635 in loop_count:1 +Warning: Failed to retrieve taxon:13489 in loop_count:1 +Warning: Failed to retrieve taxon:241587 in loop_count:1 +Warning: Failed to retrieve taxon:30461 in loop_count:1 +Warning: Failed to retrieve taxon:1240228 in loop_count:1 +Warning: Failed to retrieve taxon:8824 in loop_count:1 +Warning: Failed to retrieve taxon:8475 in loop_count:1 +Warning: Failed to retrieve taxon:9358 in loop_count:1 +Warning: Failed to retrieve taxon:51511 in loop_count:1 +Warning: Failed to retrieve taxon:7764 in loop_count:1 +Warning: Failed to retrieve taxon:2593467 in loop_count:1 +Warning: Failed to retrieve taxon:68415 in loop_count:1 +Warning: Failed to retrieve taxon:9315 in loop_count:1 +Warning: Failed to retrieve taxon:123683 in loop_count:1 +Warning: Failed to retrieve taxon:9089 in loop_count:1 +Warning: Failed to retrieve taxon:40217 in loop_count:1 +Warning: Failed to retrieve taxon:8630 in loop_count:1 +Warning: Failed to retrieve taxon:445787 in loop_count:1 +Warning: Failed to retrieve taxon:10096 in loop_count:1 +Warning: Failed to retrieve taxon:62062 in loop_count:1 +Warning: Failed to retrieve taxon:44316 in loop_count:1 +Warning: Failed to retrieve taxon:38772 in loop_count:1 +Warning: Failed to retrieve taxon:47969 in loop_count:1 +Warning: Failed to retrieve taxon:183150 in loop_count:1 +Warning: Failed to retrieve taxon:9054 in loop_count:1 +Warning: Failed to retrieve taxon:94237 in loop_count:1 +Warning: Failed to retrieve taxon:10103 in loop_count:1 +Warning: Failed to retrieve taxon:35670 in loop_count:1 +Warning: Failed to retrieve taxon:452646 in loop_count:1 +Warning: Failed to retrieve taxon:47308 in loop_count:1 +Warning: Failed to retrieve taxon:257818 in loop_count:1 +Warning: Failed to retrieve taxon:367368 in loop_count:1 +Warning: Failed to retrieve taxon:1328070 in loop_count:1 +Warning: Failed to retrieve taxon:8508 in loop_count:1 +Warning: Failed to retrieve taxon:311401 in loop_count:1 +Warning: Failed to retrieve taxon:9049 in loop_count:1 +Warning: Failed to retrieve taxon:9813 in loop_count:1 +Warning: Failed to retrieve taxon:9643 in loop_count:1 +Warning: Failed to retrieve taxon:7757 in loop_count:1 +Warning: Failed to retrieve taxon:59479 in loop_count:1 +Warning: Failed to retrieve taxon:37347 in loop_count:1 +Warning: Failed to retrieve taxon:1220523 in loop_count:1 +Warning: Failed to retrieve taxon:96440 in loop_count:1 +Warning: Failed to retrieve taxon:55149 in loop_count:1 +Warning: Failed to retrieve taxon:441215 in loop_count:1 +Warning: Failed to retrieve taxon:61221 in loop_count:1 +Warning: Failed to retrieve taxon:99837 in loop_count:1 +Warning: Failed to retrieve taxon:181631 in loop_count:1 +Warning: Failed to retrieve taxon:99883 in loop_count:1 +# Success: output/tsv/ensembl_transcript-refseq_rna.tsv is updated +> 2024-12-20T20:41:01 ensembl_transcript-refseq_rna Rule for TSV (output/tsv/ensembl_transcript-refseq_rna.tsv) ------------------------------ Investigating output/tsv/ensembl_transcript-refseq_rna.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-06 20:41:42 +0900 +timestamp: 2024-12-20 20:41:01 +0900 pre-requisites: --output/tsv/ () ---prepare:ensembl (2024-12-16 01:48:05 +0900) -latest-prerequisite time: 2024-12-16 01:48:05 +0900 +--prepare:ensembl (2024-12-20 20:41:01 +0900) +latest-prerequisite time: 2024-12-20 20:41:01 +0900 ................................ ### Update TSV for gea-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/gea-bioproject.tsv is newer than config/gea-bioproject/config.yaml # File output/tsv/gea-bioproject.tsv has no timestamp file -# File output/tsv/gea-bioproject.tsv is created 9.212761025845255 days ago (will be updated when >5 days) +# File output/tsv/gea-bioproject.tsv is created 13.999518897376099 days ago (will be updated when >5 days) ## Update config/gea-bioproject/config.yaml => output/tsv/gea-bioproject.tsv -< 2024-12-16T01:48:05 gea-bioproject +< 2024-12-20T20:41:01 gea-bioproject togoid-config config/gea-bioproject update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/gea-bioproject.tsv new file size per old 0 / 3032 = 0.0 < 0.5 -# Error: Failed to create output/tsv/gea-bioproject.tsv or created file was empty -# Failure: output/tsv/gea-bioproject.tsv is not updated -> 2024-12-16T01:50:13 gea-bioproject +# Success: output/tsv/gea-bioproject.tsv is updated +> 2024-12-20T20:41:02 gea-bioproject Rule for TSV (output/tsv/gea-bioproject.tsv) ------------------------------ Investigating output/tsv/gea-bioproject.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:41:43 +0900 +task needed: false +timestamp: 2024-12-20 20:41:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for gea-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/gea-biosample.tsv is newer than config/gea-biosample/config.yaml # File output/tsv/gea-biosample.tsv has no timestamp file -# File output/tsv/gea-biosample.tsv is created 9.214230862464653 days ago (will be updated when >5 days) +# File output/tsv/gea-biosample.tsv is created 13.999518923878403 days ago (will be updated when >5 days) ## Update config/gea-biosample/config.yaml => output/tsv/gea-biosample.tsv -< 2024-12-16T01:50:13 gea-biosample +< 2024-12-20T20:41:02 gea-biosample togoid-config config/gea-biosample update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/gea-biosample.tsv new file size per old 0 / 121104 = 0.0 < 0.5 -# Error: Failed to create output/tsv/gea-biosample.tsv or created file was empty -# Failure: output/tsv/gea-biosample.tsv is not updated -> 2024-12-16T01:52:20 gea-biosample +# Success: output/tsv/gea-biosample.tsv is updated +> 2024-12-20T20:41:02 gea-biosample Rule for TSV (output/tsv/gea-biosample.tsv) ------------------------------ Investigating output/tsv/gea-biosample.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:41:43 +0900 +task needed: false +timestamp: 2024-12-20 20:41:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for glycomotif-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/glycomotif-glytoucan.tsv is newer than config/glycomotif-glytoucan/config.yaml # File output/tsv/glycomotif-glytoucan.tsv has no timestamp file -# File output/tsv/glycomotif-glytoucan.tsv is created 121.18410769166488 days ago (will be updated when >5 days) +# File output/tsv/glycomotif-glytoucan.tsv is created 125.96792501071926 days ago (will be updated when >5 days) ## Update config/glycomotif-glytoucan/config.yaml => output/tsv/glycomotif-glytoucan.tsv -< 2024-12-16T01:52:20 glycomotif-glytoucan +< 2024-12-20T20:41:02 glycomotif-glytoucan togoid-config config/glycomotif-glytoucan update Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C11%2C10%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5Ba2122h-1b_1-5_2%2ANCC%2F3%3DO%5D%5Ba1221m-1a_1-5%5D%2F1-2-3-2-3-2-3-4-2-3-2%2Fa4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g3-h1_g4-i1_i3-j1_j4-k1&rootnode=true G64227KZ # Error: output/tsv/glycomotif-glytoucan.tsv new file size per old 0 / 2804382 = 0.0 < 0.5 # Error: Failed to create output/tsv/glycomotif-glytoucan.tsv or created file was empty # Failure: output/tsv/glycomotif-glytoucan.tsv is not updated -> 2024-12-16T01:52:52 glycomotif-glytoucan +> 2024-12-20T20:41:34 glycomotif-glytoucan Rule for TSV (output/tsv/glycomotif-glytoucan.tsv) ------------------------------ Investigating output/tsv/glycomotif-glytoucan.tsv @@ -1510,20 +1572,20 @@ task needed: true timestamp: 2024-08-16 21:27:13 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for glytoucan-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/glytoucan-doid.tsv is newer than config/glytoucan-doid/config.yaml # File output/tsv/glytoucan-doid.tsv is older than input/glytoucan/download.lock ## Update config/glytoucan-doid/config.yaml => output/tsv/glytoucan-doid.tsv -< 2024-12-16T01:52:52 glytoucan-doid +< 2024-12-20T20:41:34 glytoucan-doid togoid-config config/glytoucan-doid update # Error: output/tsv/glytoucan-doid.tsv new file size per old 0 / 4376 = 0.0 < 0.5 # Error: Failed to create output/tsv/glytoucan-doid.tsv or created file was empty # Failure: output/tsv/glytoucan-doid.tsv is not updated -> 2024-12-16T01:52:56 glytoucan-doid +> 2024-12-20T20:41:39 glytoucan-doid Rule for TSV (output/tsv/glytoucan-doid.tsv) ------------------------------ Investigating output/tsv/glytoucan-doid.tsv @@ -1532,18 +1594,14 @@ task needed: true timestamp: 2024-03-22 20:42:15 +0900 pre-requisites: --output/tsv/ () ---prepare:glytoucan (2024-12-16 01:52:56 +0900) -latest-prerequisite time: 2024-12-16 01:52:56 +0900 +--prepare:glytoucan (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for glytoucan-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for glytoucan-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/glytoucan-ncbigene.tsv is newer than config/glytoucan-ncbigene/config.yaml -# File output/tsv/glytoucan-ncbigene.tsv is older than input/glytoucan/download.lock -## Update config/glytoucan-ncbigene/config.yaml => output/tsv/glytoucan-ncbigene.tsv -< 2024-12-16T01:52:56 glytoucan-ncbigene -togoid-config config/glytoucan-ncbigene update -# Success: output/tsv/glytoucan-ncbigene.tsv is updated -> 2024-12-16T01:52:57 glytoucan-ncbigene +# File output/tsv/glytoucan-ncbigene.tsv is newer than input/glytoucan/download.lock +# => Preserving output/tsv/glytoucan-ncbigene.tsv Rule for TSV (output/tsv/glytoucan-ncbigene.tsv) ------------------------------ Investigating output/tsv/glytoucan-ncbigene.tsv @@ -1552,18 +1610,14 @@ task needed: true timestamp: 2024-12-16 01:52:57 +0900 pre-requisites: --output/tsv/ () ---prepare:glytoucan (2024-12-16 01:52:57 +0900) -latest-prerequisite time: 2024-12-16 01:52:57 +0900 +--prepare:glytoucan (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for glytoucan-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for glytoucan-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/glytoucan-uniprot.tsv is newer than config/glytoucan-uniprot/config.yaml -# File output/tsv/glytoucan-uniprot.tsv is older than input/glytoucan/download.lock -## Update config/glytoucan-uniprot/config.yaml => output/tsv/glytoucan-uniprot.tsv -< 2024-12-16T01:52:57 glytoucan-uniprot -togoid-config config/glytoucan-uniprot update -# Success: output/tsv/glytoucan-uniprot.tsv is updated -> 2024-12-16T01:52:59 glytoucan-uniprot +# File output/tsv/glytoucan-uniprot.tsv is newer than input/glytoucan/download.lock +# => Preserving output/tsv/glytoucan-uniprot.tsv Rule for TSV (output/tsv/glytoucan-uniprot.tsv) ------------------------------ Investigating output/tsv/glytoucan-uniprot.tsv @@ -1572,18 +1626,18 @@ task needed: true timestamp: 2024-12-16 01:52:59 +0900 pre-requisites: --output/tsv/ () ---prepare:glytoucan (2024-12-16 01:52:59 +0900) -latest-prerequisite time: 2024-12-16 01:52:59 +0900 +--prepare:glytoucan (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for hgnc-ccds if check_tsv_filesize false or check_config_timestamp true or check_tsv_timestamp true # File output/tsv/hgnc-ccds.tsv is older than config/hgnc-ccds/config.yaml ## Update config/hgnc-ccds/config.yaml => output/tsv/hgnc-ccds.tsv -< 2024-12-16T01:52:59 hgnc-ccds +< 2024-12-20T20:41:39 hgnc-ccds togoid-config config/hgnc-ccds update # Error: output/tsv/hgnc-ccds.tsv new file size per old 252491 / 544502 = 0.46370995882476096 < 0.5 # Failure: output/tsv/hgnc-ccds.tsv is not updated -> 2024-12-16T01:52:59 hgnc-ccds +> 2024-12-20T20:41:39 hgnc-ccds Rule for TSV (output/tsv/hgnc-ccds.tsv) ------------------------------ Investigating output/tsv/hgnc-ccds.tsv @@ -1592,18 +1646,14 @@ task needed: true timestamp: 2024-08-16 21:27:23 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:52:59 +0900) -latest-prerequisite time: 2024-12-16 01:52:59 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-ec.tsv is newer than config/hgnc-ec/config.yaml -# File output/tsv/hgnc-ec.tsv is older than input/hgnc/download.lock -## Update config/hgnc-ec/config.yaml => output/tsv/hgnc-ec.tsv -< 2024-12-16T01:52:59 hgnc-ec -togoid-config config/hgnc-ec update -# Success: output/tsv/hgnc-ec.tsv is updated -> 2024-12-16T01:53:00 hgnc-ec +# File output/tsv/hgnc-ec.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-ec.tsv Rule for TSV (output/tsv/hgnc-ec.tsv) ------------------------------ Investigating output/tsv/hgnc-ec.tsv @@ -1612,18 +1662,14 @@ task needed: true timestamp: 2024-12-16 01:53:00 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:00 +0900) -latest-prerequisite time: 2024-12-16 01:53:00 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-ensembl_gene.tsv is newer than config/hgnc-ensembl_gene/config.yaml -# File output/tsv/hgnc-ensembl_gene.tsv is older than input/hgnc/download.lock -## Update config/hgnc-ensembl_gene/config.yaml => output/tsv/hgnc-ensembl_gene.tsv -< 2024-12-16T01:53:00 hgnc-ensembl_gene -togoid-config config/hgnc-ensembl_gene update -# Success: output/tsv/hgnc-ensembl_gene.tsv is updated -> 2024-12-16T01:53:00 hgnc-ensembl_gene +# File output/tsv/hgnc-ensembl_gene.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-ensembl_gene.tsv Rule for TSV (output/tsv/hgnc-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/hgnc-ensembl_gene.tsv @@ -1632,18 +1678,14 @@ task needed: true timestamp: 2024-12-16 01:53:00 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:00 +0900) -latest-prerequisite time: 2024-12-16 01:53:00 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-hgnc_symbol if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-hgnc_symbol if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-hgnc_symbol.tsv is newer than config/hgnc-hgnc_symbol/config.yaml -# File output/tsv/hgnc-hgnc_symbol.tsv is older than input/hgnc/download.lock -## Update config/hgnc-hgnc_symbol/config.yaml => output/tsv/hgnc-hgnc_symbol.tsv -< 2024-12-16T01:53:00 hgnc-hgnc_symbol -togoid-config config/hgnc-hgnc_symbol update -# Success: output/tsv/hgnc-hgnc_symbol.tsv is updated -> 2024-12-16T01:53:01 hgnc-hgnc_symbol +# File output/tsv/hgnc-hgnc_symbol.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-hgnc_symbol.tsv Rule for TSV (output/tsv/hgnc-hgnc_symbol.tsv) ------------------------------ Investigating output/tsv/hgnc-hgnc_symbol.tsv @@ -1652,18 +1694,14 @@ task needed: true timestamp: 2024-12-16 01:53:01 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:01 +0900) -latest-prerequisite time: 2024-12-16 01:53:01 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-insdc.tsv is newer than config/hgnc-insdc/config.yaml -# File output/tsv/hgnc-insdc.tsv is older than input/hgnc/download.lock -## Update config/hgnc-insdc/config.yaml => output/tsv/hgnc-insdc.tsv -< 2024-12-16T01:53:01 hgnc-insdc -togoid-config config/hgnc-insdc update -# Success: output/tsv/hgnc-insdc.tsv is updated -> 2024-12-16T01:53:01 hgnc-insdc +# File output/tsv/hgnc-insdc.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-insdc.tsv Rule for TSV (output/tsv/hgnc-insdc.tsv) ------------------------------ Investigating output/tsv/hgnc-insdc.tsv @@ -1672,18 +1710,14 @@ task needed: true timestamp: 2024-12-16 01:53:01 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:01 +0900) -latest-prerequisite time: 2024-12-16 01:53:01 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-lrg if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-lrg if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-lrg.tsv is newer than config/hgnc-lrg/config.yaml -# File output/tsv/hgnc-lrg.tsv is older than input/hgnc/download.lock -## Update config/hgnc-lrg/config.yaml => output/tsv/hgnc-lrg.tsv -< 2024-12-16T01:53:01 hgnc-lrg -togoid-config config/hgnc-lrg update -# Success: output/tsv/hgnc-lrg.tsv is updated -> 2024-12-16T01:53:02 hgnc-lrg +# File output/tsv/hgnc-lrg.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-lrg.tsv Rule for TSV (output/tsv/hgnc-lrg.tsv) ------------------------------ Investigating output/tsv/hgnc-lrg.tsv @@ -1692,18 +1726,14 @@ task needed: true timestamp: 2024-12-16 01:53:02 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:02 +0900) -latest-prerequisite time: 2024-12-16 01:53:02 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-mgi_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-mgi_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-mgi_gene.tsv is newer than config/hgnc-mgi_gene/config.yaml -# File output/tsv/hgnc-mgi_gene.tsv is older than input/hgnc/download.lock -## Update config/hgnc-mgi_gene/config.yaml => output/tsv/hgnc-mgi_gene.tsv -< 2024-12-16T01:53:02 hgnc-mgi_gene -togoid-config config/hgnc-mgi_gene update -# Success: output/tsv/hgnc-mgi_gene.tsv is updated -> 2024-12-16T01:53:02 hgnc-mgi_gene +# File output/tsv/hgnc-mgi_gene.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-mgi_gene.tsv Rule for TSV (output/tsv/hgnc-mgi_gene.tsv) ------------------------------ Investigating output/tsv/hgnc-mgi_gene.tsv @@ -1712,18 +1742,14 @@ task needed: true timestamp: 2024-12-16 01:53:02 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:02 +0900) -latest-prerequisite time: 2024-12-16 01:53:02 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-mirbase.tsv is newer than config/hgnc-mirbase/config.yaml -# File output/tsv/hgnc-mirbase.tsv is older than input/hgnc/download.lock -## Update config/hgnc-mirbase/config.yaml => output/tsv/hgnc-mirbase.tsv -< 2024-12-16T01:53:02 hgnc-mirbase -togoid-config config/hgnc-mirbase update -# Success: output/tsv/hgnc-mirbase.tsv is updated -> 2024-12-16T01:53:03 hgnc-mirbase +# File output/tsv/hgnc-mirbase.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-mirbase.tsv Rule for TSV (output/tsv/hgnc-mirbase.tsv) ------------------------------ Investigating output/tsv/hgnc-mirbase.tsv @@ -1732,18 +1758,14 @@ task needed: true timestamp: 2024-12-16 01:53:03 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:03 +0900) -latest-prerequisite time: 2024-12-16 01:53:03 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-ncbigene.tsv is newer than config/hgnc-ncbigene/config.yaml -# File output/tsv/hgnc-ncbigene.tsv is older than input/hgnc/download.lock -## Update config/hgnc-ncbigene/config.yaml => output/tsv/hgnc-ncbigene.tsv -< 2024-12-16T01:53:03 hgnc-ncbigene -togoid-config config/hgnc-ncbigene update -# Success: output/tsv/hgnc-ncbigene.tsv is updated -> 2024-12-16T01:53:03 hgnc-ncbigene +# File output/tsv/hgnc-ncbigene.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-ncbigene.tsv Rule for TSV (output/tsv/hgnc-ncbigene.tsv) ------------------------------ Investigating output/tsv/hgnc-ncbigene.tsv @@ -1752,18 +1774,14 @@ task needed: true timestamp: 2024-12-16 01:53:03 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:03 +0900) -latest-prerequisite time: 2024-12-16 01:53:03 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-omim_gene.tsv is newer than config/hgnc-omim_gene/config.yaml -# File output/tsv/hgnc-omim_gene.tsv is older than input/hgnc/download.lock -## Update config/hgnc-omim_gene/config.yaml => output/tsv/hgnc-omim_gene.tsv -< 2024-12-16T01:53:03 hgnc-omim_gene -togoid-config config/hgnc-omim_gene update -# Success: output/tsv/hgnc-omim_gene.tsv is updated -> 2024-12-16T01:53:04 hgnc-omim_gene +# File output/tsv/hgnc-omim_gene.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-omim_gene.tsv Rule for TSV (output/tsv/hgnc-omim_gene.tsv) ------------------------------ Investigating output/tsv/hgnc-omim_gene.tsv @@ -1772,18 +1790,14 @@ task needed: true timestamp: 2024-12-16 01:53:04 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:04 +0900) -latest-prerequisite time: 2024-12-16 01:53:04 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-pubmed.tsv is newer than config/hgnc-pubmed/config.yaml -# File output/tsv/hgnc-pubmed.tsv is older than input/hgnc/download.lock -## Update config/hgnc-pubmed/config.yaml => output/tsv/hgnc-pubmed.tsv -< 2024-12-16T01:53:04 hgnc-pubmed -togoid-config config/hgnc-pubmed update -# Success: output/tsv/hgnc-pubmed.tsv is updated -> 2024-12-16T01:53:04 hgnc-pubmed +# File output/tsv/hgnc-pubmed.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-pubmed.tsv Rule for TSV (output/tsv/hgnc-pubmed.tsv) ------------------------------ Investigating output/tsv/hgnc-pubmed.tsv @@ -1792,18 +1806,14 @@ task needed: true timestamp: 2024-12-16 01:53:04 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:04 +0900) -latest-prerequisite time: 2024-12-16 01:53:04 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-refseq_genomic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-refseq_genomic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-refseq_genomic.tsv is newer than config/hgnc-refseq_genomic/config.yaml -# File output/tsv/hgnc-refseq_genomic.tsv is older than input/hgnc/download.lock -## Update config/hgnc-refseq_genomic/config.yaml => output/tsv/hgnc-refseq_genomic.tsv -< 2024-12-16T01:53:04 hgnc-refseq_genomic -togoid-config config/hgnc-refseq_genomic update -# Success: output/tsv/hgnc-refseq_genomic.tsv is updated -> 2024-12-16T01:53:05 hgnc-refseq_genomic +# File output/tsv/hgnc-refseq_genomic.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-refseq_genomic.tsv Rule for TSV (output/tsv/hgnc-refseq_genomic.tsv) ------------------------------ Investigating output/tsv/hgnc-refseq_genomic.tsv @@ -1812,17 +1822,14 @@ task needed: true timestamp: 2024-12-16 01:53:05 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 01:53:05 +0900) -latest-prerequisite time: 2024-12-16 01:53:05 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-refseq_rna if check_tsv_filesize false or check_config_timestamp true or check_tsv_timestamp true -# File output/tsv/hgnc-refseq_rna.tsv is older than config/hgnc-refseq_rna/config.yaml -## Update config/hgnc-refseq_rna/config.yaml => output/tsv/hgnc-refseq_rna.tsv -< 2024-12-16T01:53:05 hgnc-refseq_rna -togoid-config config/hgnc-refseq_rna update -# Success: output/tsv/hgnc-refseq_rna.tsv is updated -rm: remove write-protected regular file ‘output/tsv/hgnc-refseq_rna.tsv.old’? > 2024-12-16T15:21:11 hgnc-refseq_rna +### Update TSV for hgnc-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false +# File output/tsv/hgnc-refseq_rna.tsv is newer than config/hgnc-refseq_rna/config.yaml +# File output/tsv/hgnc-refseq_rna.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-refseq_rna.tsv Rule for TSV (output/tsv/hgnc-refseq_rna.tsv) ------------------------------ Investigating output/tsv/hgnc-refseq_rna.tsv @@ -1831,18 +1838,14 @@ task needed: true timestamp: 2024-12-16 01:53:05 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 15:21:11 +0900) -latest-prerequisite time: 2024-12-16 15:21:11 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-rgd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-rgd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-rgd.tsv is newer than config/hgnc-rgd/config.yaml -# File output/tsv/hgnc-rgd.tsv is older than input/hgnc/download.lock -## Update config/hgnc-rgd/config.yaml => output/tsv/hgnc-rgd.tsv -< 2024-12-16T15:21:11 hgnc-rgd -togoid-config config/hgnc-rgd update -# Success: output/tsv/hgnc-rgd.tsv is updated -> 2024-12-16T15:21:12 hgnc-rgd +# File output/tsv/hgnc-rgd.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-rgd.tsv Rule for TSV (output/tsv/hgnc-rgd.tsv) ------------------------------ Investigating output/tsv/hgnc-rgd.tsv @@ -1851,18 +1854,14 @@ task needed: true timestamp: 2024-12-16 15:21:12 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 15:21:12 +0900) -latest-prerequisite time: 2024-12-16 15:21:12 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hgnc-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hgnc-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hgnc-uniprot.tsv is newer than config/hgnc-uniprot/config.yaml -# File output/tsv/hgnc-uniprot.tsv is older than input/hgnc/download.lock -## Update config/hgnc-uniprot/config.yaml => output/tsv/hgnc-uniprot.tsv -< 2024-12-16T15:21:12 hgnc-uniprot -togoid-config config/hgnc-uniprot update -# Success: output/tsv/hgnc-uniprot.tsv is updated -> 2024-12-16T15:21:13 hgnc-uniprot +# File output/tsv/hgnc-uniprot.tsv is newer than input/hgnc/download.lock +# => Preserving output/tsv/hgnc-uniprot.tsv Rule for TSV (output/tsv/hgnc-uniprot.tsv) ------------------------------ Investigating output/tsv/hgnc-uniprot.tsv @@ -1871,8 +1870,8 @@ task needed: true timestamp: 2024-12-16 15:21:13 +0900 pre-requisites: --output/tsv/ () ---prepare:hgnc (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:hgnc (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for hmdb-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1887,8 +1886,8 @@ task needed: true timestamp: 2023-07-03 13:03:28 +0900 pre-requisites: --output/tsv/ () ---prepare:hmdb (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:hmdb (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for hmdb-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1903,8 +1902,8 @@ task needed: true timestamp: 2023-07-03 13:03:51 +0900 pre-requisites: --output/tsv/ () ---prepare:hmdb (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:hmdb (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for hmdb-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1919,8 +1918,8 @@ task needed: true timestamp: 2024-01-20 02:10:47 +0900 pre-requisites: --output/tsv/ () ---prepare:hmdb (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:hmdb (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for hmdb-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1935,8 +1934,8 @@ task needed: true timestamp: 2023-07-03 13:06:27 +0900 pre-requisites: --output/tsv/ () ---prepare:hmdb (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:hmdb (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for homologene-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -1951,39 +1950,31 @@ task needed: true timestamp: 2023-06-02 19:58:16 +0900 pre-requisites: --output/tsv/ () ---prepare:homologene (2024-12-16 15:21:13 +0900) -latest-prerequisite time: 2024-12-16 15:21:13 +0900 +--prepare:homologene (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hp_inheritance-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hp_inheritance-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hp_inheritance-omim_phenotype.tsv is newer than config/hp_inheritance-omim_phenotype/config.yaml # File output/tsv/hp_inheritance-omim_phenotype.tsv has no timestamp file -# File output/tsv/hp_inheritance-omim_phenotype.tsv is created 9.776838411893833 days ago (will be updated when >5 days) -## Update config/hp_inheritance-omim_phenotype/config.yaml => output/tsv/hp_inheritance-omim_phenotype.tsv -< 2024-12-16T15:21:13 hp_inheritance-omim_phenotype -togoid-config config/hp_inheritance-omim_phenotype update -# Success: output/tsv/hp_inheritance-omim_phenotype.tsv is updated -> 2024-12-16T15:21:14 hp_inheritance-omim_phenotype +# File output/tsv/hp_inheritance-omim_phenotype.tsv is created 4.222517952176307 days ago (will be updated when >5 days) +# => Preserving output/tsv/hp_inheritance-omim_phenotype.tsv Rule for TSV (output/tsv/hp_inheritance-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/hp_inheritance-omim_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:21:14 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for hp_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hp_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hp_phenotype-omim_phenotype.tsv is newer than config/hp_phenotype-omim_phenotype/config.yaml -# File output/tsv/hp_phenotype-omim_phenotype.tsv is older than input/hp_phenotype/download.lock -## Update config/hp_phenotype-omim_phenotype/config.yaml => output/tsv/hp_phenotype-omim_phenotype.tsv -< 2024-12-16T15:21:14 hp_phenotype-omim_phenotype -togoid-config config/hp_phenotype-omim_phenotype update -# Success: output/tsv/hp_phenotype-omim_phenotype.tsv is updated -> 2024-12-16T15:21:14 hp_phenotype-omim_phenotype +# File output/tsv/hp_phenotype-omim_phenotype.tsv is newer than input/hp_phenotype/download.lock +# => Preserving output/tsv/hp_phenotype-omim_phenotype.tsv Rule for TSV (output/tsv/hp_phenotype-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/hp_phenotype-omim_phenotype.tsv @@ -1992,18 +1983,14 @@ task needed: true timestamp: 2024-12-16 15:21:14 +0900 pre-requisites: --output/tsv/ () ---prepare:hp_phenotype (2024-12-16 15:21:14 +0900) -latest-prerequisite time: 2024-12-16 15:21:14 +0900 +--prepare:hp_phenotype (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ -### Update TSV for hp_phenotype-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for hp_phenotype-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/hp_phenotype-orphanet_phenotype.tsv is newer than config/hp_phenotype-orphanet_phenotype/config.yaml -# File output/tsv/hp_phenotype-orphanet_phenotype.tsv is older than input/hp_phenotype/download.lock -## Update config/hp_phenotype-orphanet_phenotype/config.yaml => output/tsv/hp_phenotype-orphanet_phenotype.tsv -< 2024-12-16T15:21:14 hp_phenotype-orphanet_phenotype -togoid-config config/hp_phenotype-orphanet_phenotype update -# Success: output/tsv/hp_phenotype-orphanet_phenotype.tsv is updated -> 2024-12-16T15:21:15 hp_phenotype-orphanet_phenotype +# File output/tsv/hp_phenotype-orphanet_phenotype.tsv is newer than input/hp_phenotype/download.lock +# => Preserving output/tsv/hp_phenotype-orphanet_phenotype.tsv Rule for TSV (output/tsv/hp_phenotype-orphanet_phenotype.tsv) ------------------------------ Investigating output/tsv/hp_phenotype-orphanet_phenotype.tsv @@ -2012,104 +1999,92 @@ task needed: true timestamp: 2024-12-16 15:21:15 +0900 pre-requisites: --output/tsv/ () ---prepare:hp_phenotype (2024-12-16 15:21:15 +0900) -latest-prerequisite time: 2024-12-16 15:21:15 +0900 +--prepare:hp_phenotype (2024-12-20 20:41:39 +0900) +latest-prerequisite time: 2024-12-20 20:41:39 +0900 ................................ ### Update TSV for insdc-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/insdc-bioproject.tsv is newer than config/insdc-bioproject/config.yaml # File output/tsv/insdc-bioproject.tsv has no timestamp file -# File output/tsv/insdc-bioproject.tsv is created 9.776600484627188 days ago (will be updated when >5 days) +# File output/tsv/insdc-bioproject.tsv is created 13.999100932560555 days ago (will be updated when >5 days) ## Update config/insdc-bioproject/config.yaml => output/tsv/insdc-bioproject.tsv -< 2024-12-16T15:21:15 insdc-bioproject +< 2024-12-20T20:41:39 insdc-bioproject togoid-config config/insdc-bioproject update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/insdc-bioproject.tsv new file size per old 0 / 1191557755 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc-bioproject.tsv or created file was empty -# Failure: output/tsv/insdc-bioproject.tsv is not updated -> 2024-12-16T15:23:23 insdc-bioproject +# Success: output/tsv/insdc-bioproject.tsv is updated +> 2024-12-20T20:42:02 insdc-bioproject Rule for TSV (output/tsv/insdc-bioproject.tsv) ------------------------------ Investigating output/tsv/insdc-bioproject.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:42:57 +0900 +task needed: false +timestamp: 2024-12-20 20:42:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for insdc-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/insdc-biosample.tsv is newer than config/insdc-biosample/config.yaml # File output/tsv/insdc-biosample.tsv has no timestamp file -# File output/tsv/insdc-biosample.tsv is created 9.77720530920839 days ago (will be updated when >5 days) +# File output/tsv/insdc-biosample.tsv is created 13.998497489176122 days ago (will be updated when >5 days) ## Update config/insdc-biosample/config.yaml => output/tsv/insdc-biosample.tsv -< 2024-12-16T15:23:23 insdc-biosample +< 2024-12-20T20:42:02 insdc-biosample togoid-config config/insdc-biosample update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/insdc-biosample.tsv new file size per old 0 / 4269980335 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc-biosample.tsv or created file was empty -# Failure: output/tsv/insdc-biosample.tsv is not updated -> 2024-12-16T15:25:30 insdc-biosample +# Success: output/tsv/insdc-biosample.tsv is updated +> 2024-12-20T20:43:19 insdc-biosample Rule for TSV (output/tsv/insdc-biosample.tsv) ------------------------------ Investigating output/tsv/insdc-biosample.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:12 +0900 +task needed: false +timestamp: 2024-12-20 20:43:19 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for insdc_master-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/insdc_master-bioproject.tsv is newer than config/insdc_master-bioproject/config.yaml # File output/tsv/insdc_master-bioproject.tsv has no timestamp file -# File output/tsv/insdc_master-bioproject.tsv is created 9.778663057370961 days ago (will be updated when >5 days) +# File output/tsv/insdc_master-bioproject.tsv is created 13.999372182565255 days ago (will be updated when >5 days) ## Update config/insdc_master-bioproject/config.yaml => output/tsv/insdc_master-bioproject.tsv -< 2024-12-16T15:25:30 insdc_master-bioproject +< 2024-12-20T20:43:19 insdc_master-bioproject togoid-config config/insdc_master-bioproject update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/insdc_master-bioproject.tsv new file size per old 0 / 41801168 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc_master-bioproject.tsv or created file was empty -# Failure: output/tsv/insdc_master-bioproject.tsv is not updated -> 2024-12-16T15:27:38 insdc_master-bioproject +# Success: output/tsv/insdc_master-bioproject.tsv is updated +> 2024-12-20T20:43:21 insdc_master-bioproject Rule for TSV (output/tsv/insdc_master-bioproject.tsv) ------------------------------ Investigating output/tsv/insdc_master-bioproject.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:14 +0900 +task needed: false +timestamp: 2024-12-20 20:43:21 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for insdc_master-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/insdc_master-biosample.tsv is newer than config/insdc_master-biosample/config.yaml # File output/tsv/insdc_master-biosample.tsv has no timestamp file -# File output/tsv/insdc_master-biosample.tsv is created 9.780121934212882 days ago (will be updated when >5 days) +# File output/tsv/insdc_master-biosample.tsv is created 13.999372366846792 days ago (will be updated when >5 days) ## Update config/insdc_master-biosample/config.yaml => output/tsv/insdc_master-biosample.tsv -< 2024-12-16T15:27:38 insdc_master-biosample +< 2024-12-20T20:43:21 insdc_master-biosample togoid-config config/insdc_master-biosample update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/insdc_master-biosample.tsv new file size per old 0 / 43765492 = 0.0 < 0.5 -# Error: Failed to create output/tsv/insdc_master-biosample.tsv or created file was empty -# Failure: output/tsv/insdc_master-biosample.tsv is not updated -> 2024-12-16T15:29:45 insdc_master-biosample +# Success: output/tsv/insdc_master-biosample.tsv is updated +> 2024-12-20T20:43:22 insdc_master-biosample Rule for TSV (output/tsv/insdc_master-biosample.tsv) ------------------------------ Investigating output/tsv/insdc_master-biosample.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:15 +0900 +task needed: false +timestamp: 2024-12-20 20:43:22 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for interpro-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2124,8 +2099,8 @@ task needed: true timestamp: 2024-11-29 22:27:40 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2140,8 +2115,8 @@ task needed: true timestamp: 2024-11-29 22:27:43 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2156,8 +2131,8 @@ task needed: true timestamp: 2024-11-29 22:27:44 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-prosite if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2172,8 +2147,8 @@ task needed: true timestamp: 2024-11-29 22:27:46 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2188,8 +2163,8 @@ task needed: true timestamp: 2024-11-29 22:27:48 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2204,8 +2179,8 @@ task needed: true timestamp: 2024-11-29 22:27:50 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-smart if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2220,8 +2195,8 @@ task needed: true timestamp: 2024-11-29 22:27:51 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for interpro-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -2236,88 +2211,79 @@ task needed: true timestamp: 2024-11-30 02:23:51 +0900 pre-requisites: --output/tsv/ () ---prepare:interpro (2024-12-16 15:29:45 +0900) -latest-prerequisite time: 2024-12-16 15:29:45 +0900 +--prepare:interpro (2024-12-20 20:43:22 +0900) +latest-prerequisite time: 2024-12-20 20:43:22 +0900 ................................ ### Update TSV for jga_study-jga_dataset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/jga_study-jga_dataset.tsv is newer than config/jga_study-jga_dataset/config.yaml # File output/tsv/jga_study-jga_dataset.tsv has no timestamp file -# File output/tsv/jga_study-jga_dataset.tsv is created 9.78159249394478 days ago (will be updated when >5 days) +# File output/tsv/jga_study-jga_dataset.tsv is created 13.99938539009617 days ago (will be updated when >5 days) ## Update config/jga_study-jga_dataset/config.yaml => output/tsv/jga_study-jga_dataset.tsv -< 2024-12-16T15:29:45 jga_study-jga_dataset +< 2024-12-20T20:43:22 jga_study-jga_dataset togoid-config config/jga_study-jga_dataset update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/jga_study-jga_dataset.tsv new file size per old 0 / 4378 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-jga_dataset.tsv or created file was empty -# Failure: output/tsv/jga_study-jga_dataset.tsv is not updated -> 2024-12-16T15:31:53 jga_study-jga_dataset +# Success: output/tsv/jga_study-jga_dataset.tsv is updated +> 2024-12-20T20:43:23 jga_study-jga_dataset Rule for TSV (output/tsv/jga_study-jga_dataset.tsv) ------------------------------ Investigating output/tsv/jga_study-jga_dataset.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:16 +0900 +task needed: false +timestamp: 2024-12-20 20:43:23 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for jga_study-nbdc_human_db if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/jga_study-nbdc_human_db.tsv is newer than config/jga_study-nbdc_human_db/config.yaml # File output/tsv/jga_study-nbdc_human_db.tsv has no timestamp file -# File output/tsv/jga_study-nbdc_human_db.tsv is created 9.783062965355603 days ago (will be updated when >5 days) +# File output/tsv/jga_study-nbdc_human_db.tsv is created 13.9993850961186 days ago (will be updated when >5 days) ## Update config/jga_study-nbdc_human_db/config.yaml => output/tsv/jga_study-nbdc_human_db.tsv -< 2024-12-16T15:31:53 jga_study-nbdc_human_db +< 2024-12-20T20:43:23 jga_study-nbdc_human_db togoid-config config/jga_study-nbdc_human_db update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/jga_study-nbdc_human_db.tsv new file size per old 0 / 5795 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-nbdc_human_db.tsv or created file was empty -# Failure: output/tsv/jga_study-nbdc_human_db.tsv is not updated -> 2024-12-16T15:34:00 jga_study-nbdc_human_db +# Success: output/tsv/jga_study-nbdc_human_db.tsv is updated +> 2024-12-20T20:43:23 jga_study-nbdc_human_db Rule for TSV (output/tsv/jga_study-nbdc_human_db.tsv) ------------------------------ Investigating output/tsv/jga_study-nbdc_human_db.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:16 +0900 +task needed: false +timestamp: 2024-12-20 20:43:23 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for jga_study-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/jga_study-pubmed.tsv is newer than config/jga_study-pubmed/config.yaml # File output/tsv/jga_study-pubmed.tsv has no timestamp file -# File output/tsv/jga_study-pubmed.tsv is created 9.784533419575498 days ago (will be updated when >5 days) +# File output/tsv/jga_study-pubmed.tsv is created 13.999384512272998 days ago (will be updated when >5 days) ## Update config/jga_study-pubmed/config.yaml => output/tsv/jga_study-pubmed.tsv -< 2024-12-16T15:34:00 jga_study-pubmed +< 2024-12-20T20:43:23 jga_study-pubmed togoid-config config/jga_study-pubmed update -curl: (7) Failed connect to ddbj.nig.ac.jp:443; Connection timed out -# Error: output/tsv/jga_study-pubmed.tsv new file size per old 0 / 2597 = 0.0 < 0.5 -# Error: Failed to create output/tsv/jga_study-pubmed.tsv or created file was empty -# Failure: output/tsv/jga_study-pubmed.tsv is not updated -> 2024-12-16T15:36:08 jga_study-pubmed +# Success: output/tsv/jga_study-pubmed.tsv is updated +> 2024-12-20T20:43:24 jga_study-pubmed Rule for TSV (output/tsv/jga_study-pubmed.tsv) ------------------------------ Investigating output/tsv/jga_study-pubmed.tsv class: Rake::FileTask -task needed: true -timestamp: 2024-12-06 20:44:16 +0900 +task needed: false +timestamp: 2024-12-20 20:43:24 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for lipidmaps-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/lipidmaps-chebi.tsv is newer than config/lipidmaps-chebi/config.yaml # File output/tsv/lipidmaps-chebi.tsv has no timestamp file -# File output/tsv/lipidmaps-chebi.tsv is created 86.46341337809038 days ago (will be updated when >5 days) +# File output/tsv/lipidmaps-chebi.tsv is created 90.67679402254076 days ago (will be updated when >5 days) ## Update config/lipidmaps-chebi/config.yaml => output/tsv/lipidmaps-chebi.tsv -< 2024-12-16T15:36:08 lipidmaps-chebi +< 2024-12-20T20:43:24 lipidmaps-chebi togoid-config config/lipidmaps-chebi update # Error: output/tsv/lipidmaps-chebi.tsv new file size per old 148 / 253350 = 0.000584172093941188 < 0.5 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML @@ -2333,7 +2299,7 @@ togoid-config config/lipidmaps-chebi update # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML

You don't have permission to access this resource.

# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML # Failure: output/tsv/lipidmaps-chebi.tsv is not updated -> 2024-12-16T15:36:09 lipidmaps-chebi +> 2024-12-20T20:43:27 lipidmaps-chebi Rule for TSV (output/tsv/lipidmaps-chebi.tsv) ------------------------------ Investigating output/tsv/lipidmaps-chebi.tsv @@ -2342,16 +2308,16 @@ task needed: true timestamp: 2024-09-21 04:28:49 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for lipidmaps-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/lipidmaps-inchi_key.tsv is newer than config/lipidmaps-inchi_key/config.yaml # File output/tsv/lipidmaps-inchi_key.tsv has no timestamp file -# File output/tsv/lipidmaps-inchi_key.tsv is created 86.46338789144772 days ago (will be updated when >5 days) +# File output/tsv/lipidmaps-inchi_key.tsv is created 90.67678301001752 days ago (will be updated when >5 days) ## Update config/lipidmaps-inchi_key/config.yaml => output/tsv/lipidmaps-inchi_key.tsv -< 2024-12-16T15:36:09 lipidmaps-inchi_key +< 2024-12-20T20:43:27 lipidmaps-inchi_key togoid-config config/lipidmaps-inchi_key update # Error: output/tsv/lipidmaps-inchi_key.tsv new file size per old 148 / 1976727 = 7.487123917465588e-05 < 0.5 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML @@ -2367,7 +2333,7 @@ togoid-config config/lipidmaps-inchi_key update # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML

You don't have permission to access this resource.

# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML # Failure: output/tsv/lipidmaps-inchi_key.tsv is not updated -> 2024-12-16T15:36:11 lipidmaps-inchi_key +> 2024-12-20T20:43:28 lipidmaps-inchi_key Rule for TSV (output/tsv/lipidmaps-inchi_key.tsv) ------------------------------ Investigating output/tsv/lipidmaps-inchi_key.tsv @@ -2376,16 +2342,16 @@ task needed: true timestamp: 2024-09-21 04:28:53 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for lipidmaps-swisslipids if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/lipidmaps-swisslipids.tsv is newer than config/lipidmaps-swisslipids/config.yaml # File output/tsv/lipidmaps-swisslipids.tsv has no timestamp file -# File output/tsv/lipidmaps-swisslipids.tsv is created 86.46336879690553 days ago (will be updated when >5 days) +# File output/tsv/lipidmaps-swisslipids.tsv is created 90.6767637943059 days ago (will be updated when >5 days) ## Update config/lipidmaps-swisslipids/config.yaml => output/tsv/lipidmaps-swisslipids.tsv -< 2024-12-16T15:36:11 lipidmaps-swisslipids +< 2024-12-20T20:43:28 lipidmaps-swisslipids togoid-config config/lipidmaps-swisslipids update # Error: output/tsv/lipidmaps-swisslipids.tsv new file size per old 148 / 284047 = 0.0005210405320246297 < 0.5 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML @@ -2401,7 +2367,7 @@ togoid-config config/lipidmaps-swisslipids update # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML

You don't have permission to access this resource.

# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML # Failure: output/tsv/lipidmaps-swisslipids.tsv is not updated -> 2024-12-16T15:36:12 lipidmaps-swisslipids +> 2024-12-20T20:43:29 lipidmaps-swisslipids Rule for TSV (output/tsv/lipidmaps-swisslipids.tsv) ------------------------------ Investigating output/tsv/lipidmaps-swisslipids.tsv @@ -2410,21 +2376,21 @@ task needed: true timestamp: 2024-09-21 04:28:56 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mbgd_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mbgd_gene-uniprot.tsv is newer than config/mbgd_gene-uniprot/config.yaml # File output/tsv/mbgd_gene-uniprot.tsv has no timestamp file -# File output/tsv/mbgd_gene-uniprot.tsv is created 58.7278045114042 days ago (will be updated when >5 days) +# File output/tsv/mbgd_gene-uniprot.tsv is created 62.94119957341171 days ago (will be updated when >5 days) ## Update config/mbgd_gene-uniprot/config.yaml => output/tsv/mbgd_gene-uniprot.tsv -< 2024-12-16T15:36:12 mbgd_gene-uniprot +< 2024-12-20T20:43:29 mbgd_gene-uniprot togoid-config config/mbgd_gene-uniprot update # Error: output/tsv/mbgd_gene-uniprot.tsv new file size per old 0 / 4017692184 = 0.0 < 0.5 # Error: Failed to create output/tsv/mbgd_gene-uniprot.tsv or created file was empty # Failure: output/tsv/mbgd_gene-uniprot.tsv is not updated -> 2024-12-16T15:36:15 mbgd_gene-uniprot +> 2024-12-20T20:43:33 mbgd_gene-uniprot Rule for TSV (output/tsv/mbgd_gene-uniprot.tsv) ------------------------------ Investigating output/tsv/mbgd_gene-uniprot.tsv @@ -2433,21 +2399,21 @@ task needed: true timestamp: 2024-10-18 22:08:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mbgd_organism-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mbgd_organism-taxonomy.tsv is newer than config/mbgd_organism-taxonomy/config.yaml # File output/tsv/mbgd_organism-taxonomy.tsv has no timestamp file -# File output/tsv/mbgd_organism-taxonomy.tsv is created 58.72783958399594 days ago (will be updated when >5 days) +# File output/tsv/mbgd_organism-taxonomy.tsv is created 62.94123327231632 days ago (will be updated when >5 days) ## Update config/mbgd_organism-taxonomy/config.yaml => output/tsv/mbgd_organism-taxonomy.tsv -< 2024-12-16T15:36:15 mbgd_organism-taxonomy +< 2024-12-20T20:43:33 mbgd_organism-taxonomy togoid-config config/mbgd_organism-taxonomy update # Error: output/tsv/mbgd_organism-taxonomy.tsv new file size per old 0 / 81445 = 0.0 < 0.5 # Error: Failed to create output/tsv/mbgd_organism-taxonomy.tsv or created file was empty # Failure: output/tsv/mbgd_organism-taxonomy.tsv is not updated -> 2024-12-16T15:36:18 mbgd_organism-taxonomy +> 2024-12-20T20:43:36 mbgd_organism-taxonomy Rule for TSV (output/tsv/mbgd_organism-taxonomy.tsv) ------------------------------ Investigating output/tsv/mbgd_organism-taxonomy.tsv @@ -2456,307 +2422,283 @@ task needed: true timestamp: 2024-10-18 22:08:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-hp_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-hp_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-hp_phenotype.tsv is newer than config/medgen-hp_phenotype/config.yaml # File output/tsv/medgen-hp_phenotype.tsv has no timestamp file -# File output/tsv/medgen-hp_phenotype.tsv is created 9.78599091350198 days ago (will be updated when >5 days) -## Update config/medgen-hp_phenotype/config.yaml => output/tsv/medgen-hp_phenotype.tsv -< 2024-12-16T15:36:18 medgen-hp_phenotype -togoid-config config/medgen-hp_phenotype update -# Success: output/tsv/medgen-hp_phenotype.tsv is updated -> 2024-12-16T15:36:19 medgen-hp_phenotype +# File output/tsv/medgen-hp_phenotype.tsv is created 4.213388223208889 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-hp_phenotype.tsv Rule for TSV (output/tsv/medgen-hp_phenotype.tsv) ------------------------------ Investigating output/tsv/medgen-hp_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:19 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-mesh.tsv is newer than config/medgen-mesh/config.yaml # File output/tsv/medgen-mesh.tsv has no timestamp file -# File output/tsv/medgen-mesh.tsv is created 9.78599134910492 days ago (will be updated when >5 days) -## Update config/medgen-mesh/config.yaml => output/tsv/medgen-mesh.tsv -< 2024-12-16T15:36:19 medgen-mesh -togoid-config config/medgen-mesh update -# Success: output/tsv/medgen-mesh.tsv is updated -> 2024-12-16T15:36:19 medgen-mesh +# File output/tsv/medgen-mesh.tsv is created 4.2133828591329285 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-mesh.tsv Rule for TSV (output/tsv/medgen-mesh.tsv) ------------------------------ Investigating output/tsv/medgen-mesh.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:19 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-mondo.tsv is newer than config/medgen-mondo/config.yaml # File output/tsv/medgen-mondo.tsv has no timestamp file -# File output/tsv/medgen-mondo.tsv is created 9.785991429680278 days ago (will be updated when >5 days) -## Update config/medgen-mondo/config.yaml => output/tsv/medgen-mondo.tsv -< 2024-12-16T15:36:19 medgen-mondo -togoid-config config/medgen-mondo update -# Success: output/tsv/medgen-mondo.tsv is updated -> 2024-12-16T15:36:20 medgen-mondo +# File output/tsv/medgen-mondo.tsv is created 4.213376661177685 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-mondo.tsv Rule for TSV (output/tsv/medgen-mondo.tsv) ------------------------------ Investigating output/tsv/medgen-mondo.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:20 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-ncbigene.tsv is newer than config/medgen-ncbigene/config.yaml # File output/tsv/medgen-ncbigene.tsv has no timestamp file -# File output/tsv/medgen-ncbigene.tsv is created 9.785992830367489 days ago (will be updated when >5 days) -## Update config/medgen-ncbigene/config.yaml => output/tsv/medgen-ncbigene.tsv -< 2024-12-16T15:36:20 medgen-ncbigene -togoid-config config/medgen-ncbigene update -# Success: output/tsv/medgen-ncbigene.tsv is updated -> 2024-12-16T15:36:20 medgen-ncbigene +# File output/tsv/medgen-ncbigene.tsv is created 4.213372176371679 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-ncbigene.tsv Rule for TSV (output/tsv/medgen-ncbigene.tsv) ------------------------------ Investigating output/tsv/medgen-ncbigene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:20 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-omim_phenotype.tsv is newer than config/medgen-omim_phenotype/config.yaml # File output/tsv/medgen-omim_phenotype.tsv has no timestamp file -# File output/tsv/medgen-omim_phenotype.tsv is created 9.785992481644305 days ago (will be updated when >5 days) -## Update config/medgen-omim_phenotype/config.yaml => output/tsv/medgen-omim_phenotype.tsv -< 2024-12-16T15:36:20 medgen-omim_phenotype -togoid-config config/medgen-omim_phenotype update -# Success: output/tsv/medgen-omim_phenotype.tsv is updated -> 2024-12-16T15:36:21 medgen-omim_phenotype +# File output/tsv/medgen-omim_phenotype.tsv is created 4.213367071361667 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-omim_phenotype.tsv Rule for TSV (output/tsv/medgen-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/medgen-omim_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:21 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for medgen-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for medgen-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/medgen-orphanet_phenotype.tsv is newer than config/medgen-orphanet_phenotype/config.yaml # File output/tsv/medgen-orphanet_phenotype.tsv has no timestamp file -# File output/tsv/medgen-orphanet_phenotype.tsv is created 9.78599277264456 days ago (will be updated when >5 days) -## Update config/medgen-orphanet_phenotype/config.yaml => output/tsv/medgen-orphanet_phenotype.tsv -< 2024-12-16T15:36:21 medgen-orphanet_phenotype -togoid-config config/medgen-orphanet_phenotype update -# Success: output/tsv/medgen-orphanet_phenotype.tsv is updated -> 2024-12-16T15:36:22 medgen-orphanet_phenotype +# File output/tsv/medgen-orphanet_phenotype.tsv is created 4.213354299138635 days ago (will be updated when >5 days) +# => Preserving output/tsv/medgen-orphanet_phenotype.tsv Rule for TSV (output/tsv/medgen-orphanet_phenotype.tsv) ------------------------------ Investigating output/tsv/medgen-orphanet_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:22 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mgi_gene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_gene-ensembl_gene.tsv is newer than config/mgi_gene-ensembl_gene/config.yaml # File output/tsv/mgi_gene-ensembl_gene.tsv is older than input/mgi_gene/download.lock ## Update config/mgi_gene-ensembl_gene/config.yaml => output/tsv/mgi_gene-ensembl_gene.tsv -< 2024-12-16T15:36:22 mgi_gene-ensembl_gene +< 2024-12-20T20:43:36 mgi_gene-ensembl_gene togoid-config config/mgi_gene-ensembl_gene update # Success: output/tsv/mgi_gene-ensembl_gene.tsv is updated -> 2024-12-16T15:36:22 mgi_gene-ensembl_gene +> 2024-12-20T20:43:36 mgi_gene-ensembl_gene Rule for TSV (output/tsv/mgi_gene-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/mgi_gene-ensembl_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:22 +0900 +timestamp: 2024-12-20 20:43:36 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_gene (2024-12-16 15:36:22 +0900) -latest-prerequisite time: 2024-12-16 15:36:22 +0900 +--prepare:mgi_gene (2024-12-20 20:43:36 +0900) +latest-prerequisite time: 2024-12-20 20:43:36 +0900 ................................ ### Update TSV for mgi_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_gene-hgnc.tsv is newer than config/mgi_gene-hgnc/config.yaml # File output/tsv/mgi_gene-hgnc.tsv is older than input/mgi_gene/download.lock ## Update config/mgi_gene-hgnc/config.yaml => output/tsv/mgi_gene-hgnc.tsv -< 2024-12-16T15:36:22 mgi_gene-hgnc +< 2024-12-20T20:43:36 mgi_gene-hgnc togoid-config config/mgi_gene-hgnc update # Success: output/tsv/mgi_gene-hgnc.tsv is updated -> 2024-12-16T15:36:23 mgi_gene-hgnc +> 2024-12-20T20:43:37 mgi_gene-hgnc Rule for TSV (output/tsv/mgi_gene-hgnc.tsv) ------------------------------ Investigating output/tsv/mgi_gene-hgnc.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:23 +0900 +timestamp: 2024-12-20 20:43:37 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_gene (2024-12-16 15:36:23 +0900) -latest-prerequisite time: 2024-12-16 15:36:23 +0900 +--prepare:mgi_gene (2024-12-20 20:43:37 +0900) +latest-prerequisite time: 2024-12-20 20:43:37 +0900 ................................ ### Update TSV for mgi_gene-mgi_allele if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_gene-mgi_allele.tsv is newer than config/mgi_gene-mgi_allele/config.yaml # File output/tsv/mgi_gene-mgi_allele.tsv is older than input/mgi_gene/download.lock ## Update config/mgi_gene-mgi_allele/config.yaml => output/tsv/mgi_gene-mgi_allele.tsv -< 2024-12-16T15:36:23 mgi_gene-mgi_allele +< 2024-12-20T20:43:37 mgi_gene-mgi_allele togoid-config config/mgi_gene-mgi_allele update # Success: output/tsv/mgi_gene-mgi_allele.tsv is updated -> 2024-12-16T15:36:24 mgi_gene-mgi_allele +> 2024-12-20T20:43:38 mgi_gene-mgi_allele Rule for TSV (output/tsv/mgi_gene-mgi_allele.tsv) ------------------------------ Investigating output/tsv/mgi_gene-mgi_allele.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:24 +0900 +timestamp: 2024-12-20 20:43:38 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_gene (2024-12-16 15:36:24 +0900) -latest-prerequisite time: 2024-12-16 15:36:24 +0900 +--prepare:mgi_gene (2024-12-20 20:43:38 +0900) +latest-prerequisite time: 2024-12-20 20:43:38 +0900 ................................ ### Update TSV for mgi_gene-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_gene-ncbigene.tsv is newer than config/mgi_gene-ncbigene/config.yaml # File output/tsv/mgi_gene-ncbigene.tsv is older than input/mgi_gene/download.lock ## Update config/mgi_gene-ncbigene/config.yaml => output/tsv/mgi_gene-ncbigene.tsv -< 2024-12-16T15:36:24 mgi_gene-ncbigene +< 2024-12-20T20:43:38 mgi_gene-ncbigene togoid-config config/mgi_gene-ncbigene update # Success: output/tsv/mgi_gene-ncbigene.tsv is updated -> 2024-12-16T15:36:25 mgi_gene-ncbigene +> 2024-12-20T20:43:39 mgi_gene-ncbigene Rule for TSV (output/tsv/mgi_gene-ncbigene.tsv) ------------------------------ Investigating output/tsv/mgi_gene-ncbigene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:25 +0900 +timestamp: 2024-12-20 20:43:38 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_gene (2024-12-16 15:36:25 +0900) -latest-prerequisite time: 2024-12-16 15:36:25 +0900 +--prepare:mgi_gene (2024-12-20 20:43:39 +0900) +latest-prerequisite time: 2024-12-20 20:43:39 +0900 ................................ ### Update TSV for mgi_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_gene-uniprot.tsv is newer than config/mgi_gene-uniprot/config.yaml # File output/tsv/mgi_gene-uniprot.tsv is older than input/mgi_gene/download.lock ## Update config/mgi_gene-uniprot/config.yaml => output/tsv/mgi_gene-uniprot.tsv -< 2024-12-16T15:36:25 mgi_gene-uniprot +< 2024-12-20T20:43:39 mgi_gene-uniprot togoid-config config/mgi_gene-uniprot update # Success: output/tsv/mgi_gene-uniprot.tsv is updated -> 2024-12-16T15:36:25 mgi_gene-uniprot +> 2024-12-20T20:43:39 mgi_gene-uniprot Rule for TSV (output/tsv/mgi_gene-uniprot.tsv) ------------------------------ Investigating output/tsv/mgi_gene-uniprot.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:25 +0900 +timestamp: 2024-12-20 20:43:39 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_gene (2024-12-16 15:36:25 +0900) -latest-prerequisite time: 2024-12-16 15:36:25 +0900 +--prepare:mgi_gene (2024-12-20 20:43:39 +0900) +latest-prerequisite time: 2024-12-20 20:43:39 +0900 ................................ ### Update TSV for mgi_genotype-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_genotype-doid.tsv is newer than config/mgi_genotype-doid/config.yaml # File output/tsv/mgi_genotype-doid.tsv is older than input/mgi_genotype/download.lock ## Update config/mgi_genotype-doid/config.yaml => output/tsv/mgi_genotype-doid.tsv -< 2024-12-16T15:36:25 mgi_genotype-doid +< 2024-12-20T20:43:39 mgi_genotype-doid togoid-config config/mgi_genotype-doid update # Success: output/tsv/mgi_genotype-doid.tsv is updated -> 2024-12-16T15:36:27 mgi_genotype-doid +> 2024-12-20T20:43:41 mgi_genotype-doid Rule for TSV (output/tsv/mgi_genotype-doid.tsv) ------------------------------ Investigating output/tsv/mgi_genotype-doid.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:27 +0900 +timestamp: 2024-12-20 20:43:41 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_genotype (2024-12-16 15:36:27 +0900) -latest-prerequisite time: 2024-12-16 15:36:27 +0900 +--prepare:mgi_genotype (2024-12-20 20:43:41 +0900) +latest-prerequisite time: 2024-12-20 20:43:41 +0900 ................................ ### Update TSV for mgi_genotype-mgi_allele if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_genotype-mgi_allele.tsv is newer than config/mgi_genotype-mgi_allele/config.yaml # File output/tsv/mgi_genotype-mgi_allele.tsv is older than input/mgi_genotype/download.lock ## Update config/mgi_genotype-mgi_allele/config.yaml => output/tsv/mgi_genotype-mgi_allele.tsv -< 2024-12-16T15:36:27 mgi_genotype-mgi_allele +< 2024-12-20T20:43:41 mgi_genotype-mgi_allele togoid-config config/mgi_genotype-mgi_allele update # Success: output/tsv/mgi_genotype-mgi_allele.tsv is updated -> 2024-12-16T15:36:28 mgi_genotype-mgi_allele +> 2024-12-20T20:43:43 mgi_genotype-mgi_allele Rule for TSV (output/tsv/mgi_genotype-mgi_allele.tsv) ------------------------------ Investigating output/tsv/mgi_genotype-mgi_allele.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:28 +0900 +timestamp: 2024-12-20 20:43:43 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_genotype (2024-12-16 15:36:28 +0900) -latest-prerequisite time: 2024-12-16 15:36:28 +0900 +--prepare:mgi_genotype (2024-12-20 20:43:43 +0900) +latest-prerequisite time: 2024-12-20 20:43:43 +0900 ................................ ### Update TSV for mgi_genotype-mp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mgi_genotype-mp.tsv is newer than config/mgi_genotype-mp/config.yaml # File output/tsv/mgi_genotype-mp.tsv is older than input/mgi_genotype/download.lock ## Update config/mgi_genotype-mp/config.yaml => output/tsv/mgi_genotype-mp.tsv -< 2024-12-16T15:36:28 mgi_genotype-mp +< 2024-12-20T20:43:43 mgi_genotype-mp togoid-config config/mgi_genotype-mp update # Success: output/tsv/mgi_genotype-mp.tsv is updated -> 2024-12-16T15:36:31 mgi_genotype-mp +> 2024-12-20T20:43:45 mgi_genotype-mp Rule for TSV (output/tsv/mgi_genotype-mp.tsv) ------------------------------ Investigating output/tsv/mgi_genotype-mp.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:36:31 +0900 +timestamp: 2024-12-20 20:43:45 +0900 pre-requisites: --output/tsv/ () ---prepare:mgi_genotype (2024-12-16 15:36:31 +0900) -latest-prerequisite time: 2024-12-16 15:36:31 +0900 +--prepare:mgi_genotype (2024-12-20 20:43:45 +0900) +latest-prerequisite time: 2024-12-20 20:43:45 +0900 ................................ ### Update TSV for mondo-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-doid.tsv is newer than config/mondo-doid/config.yaml # File output/tsv/mondo-doid.tsv has no timestamp file -# File output/tsv/mondo-doid.tsv is created 205.01928578893052 days ago (will be updated when >5 days) +# File output/tsv/mondo-doid.tsv is created 209.23264528153084 days ago (will be updated when >5 days) ## Update config/mondo-doid/config.yaml => output/tsv/mondo-doid.tsv -< 2024-12-16T15:36:31 mondo-doid +< 2024-12-20T20:43:45 mondo-doid togoid-config config/mondo-doid update # Error: output/tsv/mondo-doid.tsv new file size per old 0 / 155460 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-doid.tsv or created file was empty # Failure: output/tsv/mondo-doid.tsv is not updated -> 2024-12-16T15:36:31 mondo-doid +> 2024-12-20T20:43:45 mondo-doid Rule for TSV (output/tsv/mondo-doid.tsv) ------------------------------ Investigating output/tsv/mondo-doid.tsv @@ -2765,21 +2707,21 @@ task needed: true timestamp: 2024-05-25 15:08:45 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mondo-hp_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-hp_phenotype.tsv is newer than config/mondo-hp_phenotype/config.yaml # File output/tsv/mondo-hp_phenotype.tsv has no timestamp file -# File output/tsv/mondo-hp_phenotype.tsv is created 205.01928368365486 days ago (will be updated when >5 days) +# File output/tsv/mondo-hp_phenotype.tsv is created 209.2326442601414 days ago (will be updated when >5 days) ## Update config/mondo-hp_phenotype/config.yaml => output/tsv/mondo-hp_phenotype.tsv -< 2024-12-16T15:36:31 mondo-hp_phenotype +< 2024-12-20T20:43:45 mondo-hp_phenotype togoid-config config/mondo-hp_phenotype update # Error: output/tsv/mondo-hp_phenotype.tsv new file size per old 0 / 9184 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-hp_phenotype.tsv or created file was empty # Failure: output/tsv/mondo-hp_phenotype.tsv is not updated -> 2024-12-16T15:36:32 mondo-hp_phenotype +> 2024-12-20T20:43:46 mondo-hp_phenotype Rule for TSV (output/tsv/mondo-hp_phenotype.tsv) ------------------------------ Investigating output/tsv/mondo-hp_phenotype.tsv @@ -2788,21 +2730,21 @@ task needed: true timestamp: 2024-05-25 15:08:45 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mondo-meddra if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-meddra.tsv is newer than config/mondo-meddra/config.yaml # File output/tsv/mondo-meddra.tsv has no timestamp file -# File output/tsv/mondo-meddra.tsv is created 205.0192836662879 days ago (will be updated when >5 days) +# File output/tsv/mondo-meddra.tsv is created 209.2326446121227 days ago (will be updated when >5 days) ## Update config/mondo-meddra/config.yaml => output/tsv/mondo-meddra.tsv -< 2024-12-16T15:36:32 mondo-meddra +< 2024-12-20T20:43:46 mondo-meddra togoid-config config/mondo-meddra update # Error: output/tsv/mondo-meddra.tsv new file size per old 0 / 25262 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-meddra.tsv or created file was empty # Failure: output/tsv/mondo-meddra.tsv is not updated -> 2024-12-16T15:36:32 mondo-meddra +> 2024-12-20T20:43:46 mondo-meddra Rule for TSV (output/tsv/mondo-meddra.tsv) ------------------------------ Investigating output/tsv/mondo-meddra.tsv @@ -2811,21 +2753,21 @@ task needed: true timestamp: 2024-05-25 15:08:45 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mondo-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-mesh.tsv is newer than config/mondo-mesh/config.yaml # File output/tsv/mondo-mesh.tsv has no timestamp file -# File output/tsv/mondo-mesh.tsv is created 205.0192830672745 days ago (will be updated when >5 days) +# File output/tsv/mondo-mesh.tsv is created 209.23264395281805 days ago (will be updated when >5 days) ## Update config/mondo-mesh/config.yaml => output/tsv/mondo-mesh.tsv -< 2024-12-16T15:36:32 mondo-mesh +< 2024-12-20T20:43:46 mondo-mesh togoid-config config/mondo-mesh update # Error: output/tsv/mondo-mesh.tsv new file size per old 0 / 133836 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-mesh.tsv or created file was empty # Failure: output/tsv/mondo-mesh.tsv is not updated -> 2024-12-16T15:36:32 mondo-mesh +> 2024-12-20T20:43:47 mondo-mesh Rule for TSV (output/tsv/mondo-mesh.tsv) ------------------------------ Investigating output/tsv/mondo-mesh.tsv @@ -2834,21 +2776,21 @@ task needed: true timestamp: 2024-05-25 15:08:46 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mondo-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-omim_phenotype.tsv is newer than config/mondo-omim_phenotype/config.yaml # File output/tsv/mondo-omim_phenotype.tsv has no timestamp file -# File output/tsv/mondo-omim_phenotype.tsv is created 205.01928378979937 days ago (will be updated when >5 days) +# File output/tsv/mondo-omim_phenotype.tsv is created 209.23264422479582 days ago (will be updated when >5 days) ## Update config/mondo-omim_phenotype/config.yaml => output/tsv/mondo-omim_phenotype.tsv -< 2024-12-16T15:36:32 mondo-omim_phenotype +< 2024-12-20T20:43:47 mondo-omim_phenotype togoid-config config/mondo-omim_phenotype update # Error: output/tsv/mondo-omim_phenotype.tsv new file size per old 0 / 145395 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-omim_phenotype.tsv or created file was empty # Failure: output/tsv/mondo-omim_phenotype.tsv is not updated -> 2024-12-16T15:36:33 mondo-omim_phenotype +> 2024-12-20T20:43:47 mondo-omim_phenotype Rule for TSV (output/tsv/mondo-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/mondo-omim_phenotype.tsv @@ -2857,21 +2799,21 @@ task needed: true timestamp: 2024-05-25 15:08:46 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for mondo-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/mondo-orphanet_phenotype.tsv is newer than config/mondo-orphanet_phenotype/config.yaml # File output/tsv/mondo-orphanet_phenotype.tsv has no timestamp file -# File output/tsv/mondo-orphanet_phenotype.tsv is created 205.01928374080936 days ago (will be updated when >5 days) +# File output/tsv/mondo-orphanet_phenotype.tsv is created 209.2326441458036 days ago (will be updated when >5 days) ## Update config/mondo-orphanet_phenotype/config.yaml => output/tsv/mondo-orphanet_phenotype.tsv -< 2024-12-16T15:36:33 mondo-orphanet_phenotype +< 2024-12-20T20:43:47 mondo-orphanet_phenotype togoid-config config/mondo-orphanet_phenotype update # Error: output/tsv/mondo-orphanet_phenotype.tsv new file size per old 0 / 146923 = 0.0 < 0.5 # Error: Failed to create output/tsv/mondo-orphanet_phenotype.tsv or created file was empty # Failure: output/tsv/mondo-orphanet_phenotype.tsv is not updated -> 2024-12-16T15:36:33 mondo-orphanet_phenotype +> 2024-12-20T20:43:48 mondo-orphanet_phenotype Rule for TSV (output/tsv/mondo-orphanet_phenotype.tsv) ------------------------------ Investigating output/tsv/mondo-orphanet_phenotype.tsv @@ -2880,450 +2822,442 @@ task needed: true timestamp: 2024-05-25 15:08:47 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for nando-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for nando-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/nando-mondo.tsv is newer than config/nando-mondo/config.yaml # File output/tsv/nando-mondo.tsv has no timestamp file -# File output/tsv/nando-mondo.tsv is created 9.786106157317755 days ago (will be updated when >5 days) -## Update config/nando-mondo/config.yaml => output/tsv/nando-mondo.tsv -< 2024-12-16T15:36:33 nando-mondo -togoid-config config/nando-mondo update -# Success: output/tsv/nando-mondo.tsv is updated -> 2024-12-16T15:36:34 nando-mondo +# File output/tsv/nando-mondo.tsv is created 4.21335534075353 days ago (will be updated when >5 days) +# => Preserving output/tsv/nando-mondo.tsv Rule for TSV (output/tsv/nando-mondo.tsv) ------------------------------ Investigating output/tsv/nando-mondo.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 15:36:34 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for ncbigene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-ensembl_gene.tsv is newer than config/ncbigene-ensembl_gene/config.yaml # File output/tsv/ncbigene-ensembl_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-ensembl_gene/config.yaml => output/tsv/ncbigene-ensembl_gene.tsv -< 2024-12-16T15:36:34 ncbigene-ensembl_gene +< 2024-12-20T20:43:48 ncbigene-ensembl_gene togoid-config config/ncbigene-ensembl_gene update # Success: output/tsv/ncbigene-ensembl_gene.tsv is updated -> 2024-12-16T15:37:09 ncbigene-ensembl_gene +> 2024-12-20T20:44:25 ncbigene-ensembl_gene Rule for TSV (output/tsv/ncbigene-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-ensembl_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:37:09 +0900 +timestamp: 2024-12-20 20:44:25 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:37:09 +0900) -latest-prerequisite time: 2024-12-16 15:37:09 +0900 +--prepare:ncbigene (2024-12-20 20:44:25 +0900) +latest-prerequisite time: 2024-12-20 20:44:25 +0900 ................................ ### Update TSV for ncbigene-ensembl_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-ensembl_protein.tsv is newer than config/ncbigene-ensembl_protein/config.yaml # File output/tsv/ncbigene-ensembl_protein.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-ensembl_protein/config.yaml => output/tsv/ncbigene-ensembl_protein.tsv -< 2024-12-16T15:37:09 ncbigene-ensembl_protein +< 2024-12-20T20:44:25 ncbigene-ensembl_protein togoid-config config/ncbigene-ensembl_protein update # Success: output/tsv/ncbigene-ensembl_protein.tsv is updated -> 2024-12-16T15:38:21 ncbigene-ensembl_protein +> 2024-12-20T20:45:34 ncbigene-ensembl_protein Rule for TSV (output/tsv/ncbigene-ensembl_protein.tsv) ------------------------------ Investigating output/tsv/ncbigene-ensembl_protein.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:38:21 +0900 +timestamp: 2024-12-20 20:45:34 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:38:21 +0900) -latest-prerequisite time: 2024-12-16 15:38:21 +0900 +--prepare:ncbigene (2024-12-20 20:45:34 +0900) +latest-prerequisite time: 2024-12-20 20:45:34 +0900 ................................ ### Update TSV for ncbigene-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-ensembl_transcript.tsv is newer than config/ncbigene-ensembl_transcript/config.yaml # File output/tsv/ncbigene-ensembl_transcript.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-ensembl_transcript/config.yaml => output/tsv/ncbigene-ensembl_transcript.tsv -< 2024-12-16T15:38:21 ncbigene-ensembl_transcript +< 2024-12-20T20:45:34 ncbigene-ensembl_transcript togoid-config config/ncbigene-ensembl_transcript update # Success: output/tsv/ncbigene-ensembl_transcript.tsv is updated -> 2024-12-16T15:39:28 ncbigene-ensembl_transcript +> 2024-12-20T20:46:42 ncbigene-ensembl_transcript Rule for TSV (output/tsv/ncbigene-ensembl_transcript.tsv) ------------------------------ Investigating output/tsv/ncbigene-ensembl_transcript.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:39:28 +0900 +timestamp: 2024-12-20 20:46:42 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:39:28 +0900) -latest-prerequisite time: 2024-12-16 15:39:28 +0900 +--prepare:ncbigene (2024-12-20 20:46:42 +0900) +latest-prerequisite time: 2024-12-20 20:46:42 +0900 ................................ ### Update TSV for ncbigene-flybase_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-flybase_gene.tsv is newer than config/ncbigene-flybase_gene/config.yaml # File output/tsv/ncbigene-flybase_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-flybase_gene/config.yaml => output/tsv/ncbigene-flybase_gene.tsv -< 2024-12-16T15:39:28 ncbigene-flybase_gene +< 2024-12-20T20:46:42 ncbigene-flybase_gene togoid-config config/ncbigene-flybase_gene update # Success: output/tsv/ncbigene-flybase_gene.tsv is updated -> 2024-12-16T15:40:51 ncbigene-flybase_gene +> 2024-12-20T20:48:14 ncbigene-flybase_gene Rule for TSV (output/tsv/ncbigene-flybase_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-flybase_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:40:51 +0900 +timestamp: 2024-12-20 20:48:14 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:40:51 +0900) -latest-prerequisite time: 2024-12-16 15:40:51 +0900 +--prepare:ncbigene (2024-12-20 20:48:14 +0900) +latest-prerequisite time: 2024-12-20 20:48:14 +0900 ................................ ### Update TSV for ncbigene-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-go.tsv is newer than config/ncbigene-go/config.yaml # File output/tsv/ncbigene-go.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-go/config.yaml => output/tsv/ncbigene-go.tsv -< 2024-12-16T15:40:51 ncbigene-go +< 2024-12-20T20:48:14 ncbigene-go togoid-config config/ncbigene-go update # Success: output/tsv/ncbigene-go.tsv is updated -> 2024-12-16T15:47:16 ncbigene-go +> 2024-12-20T20:55:20 ncbigene-go Rule for TSV (output/tsv/ncbigene-go.tsv) ------------------------------ Investigating output/tsv/ncbigene-go.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:47:16 +0900 +timestamp: 2024-12-20 20:55:20 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:47:16 +0900) -latest-prerequisite time: 2024-12-16 15:47:16 +0900 +--prepare:ncbigene (2024-12-20 20:55:20 +0900) +latest-prerequisite time: 2024-12-20 20:55:20 +0900 ................................ ### Update TSV for ncbigene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-hgnc.tsv is newer than config/ncbigene-hgnc/config.yaml # File output/tsv/ncbigene-hgnc.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-hgnc/config.yaml => output/tsv/ncbigene-hgnc.tsv -< 2024-12-16T15:47:16 ncbigene-hgnc +< 2024-12-20T20:55:20 ncbigene-hgnc togoid-config config/ncbigene-hgnc update # Success: output/tsv/ncbigene-hgnc.tsv is updated -> 2024-12-16T15:47:17 ncbigene-hgnc +> 2024-12-20T20:55:21 ncbigene-hgnc Rule for TSV (output/tsv/ncbigene-hgnc.tsv) ------------------------------ Investigating output/tsv/ncbigene-hgnc.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:47:17 +0900 +timestamp: 2024-12-20 20:55:21 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:47:17 +0900) -latest-prerequisite time: 2024-12-16 15:47:17 +0900 +--prepare:ncbigene (2024-12-20 20:55:21 +0900) +latest-prerequisite time: 2024-12-20 20:55:21 +0900 ................................ ### Update TSV for ncbigene-mgi_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-mgi_gene.tsv is newer than config/ncbigene-mgi_gene/config.yaml # File output/tsv/ncbigene-mgi_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-mgi_gene/config.yaml => output/tsv/ncbigene-mgi_gene.tsv -< 2024-12-16T15:47:17 ncbigene-mgi_gene +< 2024-12-20T20:55:21 ncbigene-mgi_gene togoid-config config/ncbigene-mgi_gene update # Success: output/tsv/ncbigene-mgi_gene.tsv is updated -> 2024-12-16T15:48:26 ncbigene-mgi_gene +> 2024-12-20T20:56:33 ncbigene-mgi_gene Rule for TSV (output/tsv/ncbigene-mgi_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-mgi_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:48:26 +0900 +timestamp: 2024-12-20 20:56:33 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:48:26 +0900) -latest-prerequisite time: 2024-12-16 15:48:26 +0900 +--prepare:ncbigene (2024-12-20 20:56:33 +0900) +latest-prerequisite time: 2024-12-20 20:56:33 +0900 ................................ ### Update TSV for ncbigene-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-mirbase.tsv is newer than config/ncbigene-mirbase/config.yaml # File output/tsv/ncbigene-mirbase.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-mirbase/config.yaml => output/tsv/ncbigene-mirbase.tsv -< 2024-12-16T15:48:26 ncbigene-mirbase +< 2024-12-20T20:56:33 ncbigene-mirbase togoid-config config/ncbigene-mirbase update # Success: output/tsv/ncbigene-mirbase.tsv is updated -> 2024-12-16T15:50:19 ncbigene-mirbase +> 2024-12-20T20:58:27 ncbigene-mirbase Rule for TSV (output/tsv/ncbigene-mirbase.tsv) ------------------------------ Investigating output/tsv/ncbigene-mirbase.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:50:19 +0900 +timestamp: 2024-12-20 20:58:27 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:50:19 +0900) -latest-prerequisite time: 2024-12-16 15:50:19 +0900 +--prepare:ncbigene (2024-12-20 20:58:27 +0900) +latest-prerequisite time: 2024-12-20 20:58:27 +0900 ................................ ### Update TSV for ncbigene-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-omim_gene.tsv is newer than config/ncbigene-omim_gene/config.yaml # File output/tsv/ncbigene-omim_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-omim_gene/config.yaml => output/tsv/ncbigene-omim_gene.tsv -< 2024-12-16T15:50:19 ncbigene-omim_gene +< 2024-12-20T20:58:27 ncbigene-omim_gene togoid-config config/ncbigene-omim_gene update # Success: output/tsv/ncbigene-omim_gene.tsv is updated -> 2024-12-16T15:50:20 ncbigene-omim_gene +> 2024-12-20T20:58:27 ncbigene-omim_gene Rule for TSV (output/tsv/ncbigene-omim_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-omim_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:50:20 +0900 +timestamp: 2024-12-20 20:58:27 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:50:20 +0900) -latest-prerequisite time: 2024-12-16 15:50:20 +0900 +--prepare:ncbigene (2024-12-20 20:58:27 +0900) +latest-prerequisite time: 2024-12-20 20:58:27 +0900 ................................ ### Update TSV for ncbigene-refseq_genomic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-refseq_genomic.tsv is newer than config/ncbigene-refseq_genomic/config.yaml # File output/tsv/ncbigene-refseq_genomic.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-refseq_genomic/config.yaml => output/tsv/ncbigene-refseq_genomic.tsv -< 2024-12-16T15:50:20 ncbigene-refseq_genomic +< 2024-12-20T20:58:27 ncbigene-refseq_genomic togoid-config config/ncbigene-refseq_genomic update # Success: output/tsv/ncbigene-refseq_genomic.tsv is updated -> 2024-12-16T15:55:05 ncbigene-refseq_genomic +> 2024-12-20T21:03:20 ncbigene-refseq_genomic Rule for TSV (output/tsv/ncbigene-refseq_genomic.tsv) ------------------------------ Investigating output/tsv/ncbigene-refseq_genomic.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 15:55:05 +0900 +timestamp: 2024-12-20 21:03:20 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 15:55:05 +0900) -latest-prerequisite time: 2024-12-16 15:55:05 +0900 +--prepare:ncbigene (2024-12-20 21:03:20 +0900) +latest-prerequisite time: 2024-12-20 21:03:20 +0900 ................................ ### Update TSV for ncbigene-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-refseq_protein.tsv is newer than config/ncbigene-refseq_protein/config.yaml # File output/tsv/ncbigene-refseq_protein.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-refseq_protein/config.yaml => output/tsv/ncbigene-refseq_protein.tsv -< 2024-12-16T15:55:05 ncbigene-refseq_protein +< 2024-12-20T21:03:20 ncbigene-refseq_protein togoid-config config/ncbigene-refseq_protein update # Success: output/tsv/ncbigene-refseq_protein.tsv is updated -> 2024-12-16T16:00:30 ncbigene-refseq_protein +> 2024-12-20T21:09:10 ncbigene-refseq_protein Rule for TSV (output/tsv/ncbigene-refseq_protein.tsv) ------------------------------ Investigating output/tsv/ncbigene-refseq_protein.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:00:30 +0900 +timestamp: 2024-12-20 21:09:10 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:00:30 +0900) -latest-prerequisite time: 2024-12-16 16:00:30 +0900 +--prepare:ncbigene (2024-12-20 21:09:10 +0900) +latest-prerequisite time: 2024-12-20 21:09:10 +0900 ................................ ### Update TSV for ncbigene-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-refseq_rna.tsv is newer than config/ncbigene-refseq_rna/config.yaml # File output/tsv/ncbigene-refseq_rna.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-refseq_rna/config.yaml => output/tsv/ncbigene-refseq_rna.tsv -< 2024-12-16T16:00:30 ncbigene-refseq_rna +< 2024-12-20T21:09:10 ncbigene-refseq_rna togoid-config config/ncbigene-refseq_rna update # Success: output/tsv/ncbigene-refseq_rna.tsv is updated -> 2024-12-16T16:05:07 ncbigene-refseq_rna +> 2024-12-20T21:13:58 ncbigene-refseq_rna Rule for TSV (output/tsv/ncbigene-refseq_rna.tsv) ------------------------------ Investigating output/tsv/ncbigene-refseq_rna.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:05:07 +0900 +timestamp: 2024-12-20 21:13:58 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:05:07 +0900) -latest-prerequisite time: 2024-12-16 16:05:07 +0900 +--prepare:ncbigene (2024-12-20 21:13:58 +0900) +latest-prerequisite time: 2024-12-20 21:13:58 +0900 ................................ ### Update TSV for ncbigene-rgd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-rgd.tsv is newer than config/ncbigene-rgd/config.yaml # File output/tsv/ncbigene-rgd.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-rgd/config.yaml => output/tsv/ncbigene-rgd.tsv -< 2024-12-16T16:05:07 ncbigene-rgd +< 2024-12-20T21:13:58 ncbigene-rgd togoid-config config/ncbigene-rgd update # Success: output/tsv/ncbigene-rgd.tsv is updated -> 2024-12-16T16:06:15 ncbigene-rgd +> 2024-12-20T21:15:07 ncbigene-rgd Rule for TSV (output/tsv/ncbigene-rgd.tsv) ------------------------------ Investigating output/tsv/ncbigene-rgd.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:06:15 +0900 +timestamp: 2024-12-20 21:15:07 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:06:15 +0900) -latest-prerequisite time: 2024-12-16 16:06:15 +0900 +--prepare:ncbigene (2024-12-20 21:15:07 +0900) +latest-prerequisite time: 2024-12-20 21:15:07 +0900 ................................ ### Update TSV for ncbigene-sgd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-sgd.tsv is newer than config/ncbigene-sgd/config.yaml # File output/tsv/ncbigene-sgd.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-sgd/config.yaml => output/tsv/ncbigene-sgd.tsv -< 2024-12-16T16:06:15 ncbigene-sgd +< 2024-12-20T21:15:07 ncbigene-sgd togoid-config config/ncbigene-sgd update # Success: output/tsv/ncbigene-sgd.tsv is updated -> 2024-12-16T16:07:34 ncbigene-sgd +> 2024-12-20T21:16:26 ncbigene-sgd Rule for TSV (output/tsv/ncbigene-sgd.tsv) ------------------------------ Investigating output/tsv/ncbigene-sgd.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:07:34 +0900 +timestamp: 2024-12-20 21:16:26 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:07:34 +0900) -latest-prerequisite time: 2024-12-16 16:07:34 +0900 +--prepare:ncbigene (2024-12-20 21:16:26 +0900) +latest-prerequisite time: 2024-12-20 21:16:26 +0900 ................................ ### Update TSV for ncbigene-tair if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-tair.tsv is newer than config/ncbigene-tair/config.yaml # File output/tsv/ncbigene-tair.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-tair/config.yaml => output/tsv/ncbigene-tair.tsv -< 2024-12-16T16:07:34 ncbigene-tair +< 2024-12-20T21:16:26 ncbigene-tair togoid-config config/ncbigene-tair update # Success: output/tsv/ncbigene-tair.tsv is updated -> 2024-12-16T16:08:52 ncbigene-tair +> 2024-12-20T21:17:48 ncbigene-tair Rule for TSV (output/tsv/ncbigene-tair.tsv) ------------------------------ Investigating output/tsv/ncbigene-tair.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:08:52 +0900 +timestamp: 2024-12-20 21:17:48 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:08:52 +0900) -latest-prerequisite time: 2024-12-16 16:08:52 +0900 +--prepare:ncbigene (2024-12-20 21:17:48 +0900) +latest-prerequisite time: 2024-12-20 21:17:48 +0900 ................................ ### Update TSV for ncbigene-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-taxonomy.tsv is newer than config/ncbigene-taxonomy/config.yaml # File output/tsv/ncbigene-taxonomy.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-taxonomy/config.yaml => output/tsv/ncbigene-taxonomy.tsv -< 2024-12-16T16:08:52 ncbigene-taxonomy +< 2024-12-20T21:17:48 ncbigene-taxonomy togoid-config config/ncbigene-taxonomy update # Success: output/tsv/ncbigene-taxonomy.tsv is updated -> 2024-12-16T16:09:42 ncbigene-taxonomy +> 2024-12-20T21:18:38 ncbigene-taxonomy Rule for TSV (output/tsv/ncbigene-taxonomy.tsv) ------------------------------ Investigating output/tsv/ncbigene-taxonomy.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:09:42 +0900 +timestamp: 2024-12-20 21:18:38 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:09:42 +0900) -latest-prerequisite time: 2024-12-16 16:09:42 +0900 +--prepare:ncbigene (2024-12-20 21:18:38 +0900) +latest-prerequisite time: 2024-12-20 21:18:38 +0900 ................................ ### Update TSV for ncbigene-vgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-vgnc.tsv is newer than config/ncbigene-vgnc/config.yaml # File output/tsv/ncbigene-vgnc.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-vgnc/config.yaml => output/tsv/ncbigene-vgnc.tsv -< 2024-12-16T16:09:42 ncbigene-vgnc +< 2024-12-20T21:18:38 ncbigene-vgnc togoid-config config/ncbigene-vgnc update # Success: output/tsv/ncbigene-vgnc.tsv is updated -> 2024-12-16T16:11:01 ncbigene-vgnc +> 2024-12-20T21:19:57 ncbigene-vgnc Rule for TSV (output/tsv/ncbigene-vgnc.tsv) ------------------------------ Investigating output/tsv/ncbigene-vgnc.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:11:01 +0900 +timestamp: 2024-12-20 21:19:57 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:11:01 +0900) -latest-prerequisite time: 2024-12-16 16:11:01 +0900 +--prepare:ncbigene (2024-12-20 21:19:57 +0900) +latest-prerequisite time: 2024-12-20 21:19:57 +0900 ................................ ### Update TSV for ncbigene-wormbase_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-wormbase_gene.tsv is newer than config/ncbigene-wormbase_gene/config.yaml # File output/tsv/ncbigene-wormbase_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-wormbase_gene/config.yaml => output/tsv/ncbigene-wormbase_gene.tsv -< 2024-12-16T16:11:01 ncbigene-wormbase_gene +< 2024-12-20T21:19:57 ncbigene-wormbase_gene togoid-config config/ncbigene-wormbase_gene update # Success: output/tsv/ncbigene-wormbase_gene.tsv is updated -> 2024-12-16T16:12:20 ncbigene-wormbase_gene +> 2024-12-20T21:21:16 ncbigene-wormbase_gene Rule for TSV (output/tsv/ncbigene-wormbase_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-wormbase_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:12:20 +0900 +timestamp: 2024-12-20 21:21:16 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:12:20 +0900) -latest-prerequisite time: 2024-12-16 16:12:20 +0900 +--prepare:ncbigene (2024-12-20 21:21:16 +0900) +latest-prerequisite time: 2024-12-20 21:21:16 +0900 ................................ ### Update TSV for ncbigene-xenbase_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-xenbase_gene.tsv is newer than config/ncbigene-xenbase_gene/config.yaml # File output/tsv/ncbigene-xenbase_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-xenbase_gene/config.yaml => output/tsv/ncbigene-xenbase_gene.tsv -< 2024-12-16T16:12:20 ncbigene-xenbase_gene +< 2024-12-20T21:21:16 ncbigene-xenbase_gene togoid-config config/ncbigene-xenbase_gene update # Success: output/tsv/ncbigene-xenbase_gene.tsv is updated -> 2024-12-16T16:13:38 ncbigene-xenbase_gene +> 2024-12-20T21:22:40 ncbigene-xenbase_gene Rule for TSV (output/tsv/ncbigene-xenbase_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-xenbase_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:13:38 +0900 +timestamp: 2024-12-20 21:22:40 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:13:38 +0900) -latest-prerequisite time: 2024-12-16 16:13:38 +0900 +--prepare:ncbigene (2024-12-20 21:22:40 +0900) +latest-prerequisite time: 2024-12-20 21:22:40 +0900 ................................ ### Update TSV for ncbigene-zfin_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/ncbigene-zfin_gene.tsv is newer than config/ncbigene-zfin_gene/config.yaml # File output/tsv/ncbigene-zfin_gene.tsv is older than input/ncbigene/download.lock ## Update config/ncbigene-zfin_gene/config.yaml => output/tsv/ncbigene-zfin_gene.tsv -< 2024-12-16T16:13:38 ncbigene-zfin_gene +< 2024-12-20T21:22:40 ncbigene-zfin_gene togoid-config config/ncbigene-zfin_gene update # Success: output/tsv/ncbigene-zfin_gene.tsv is updated -> 2024-12-16T16:14:56 ncbigene-zfin_gene +> 2024-12-20T21:23:59 ncbigene-zfin_gene Rule for TSV (output/tsv/ncbigene-zfin_gene.tsv) ------------------------------ Investigating output/tsv/ncbigene-zfin_gene.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:14:56 +0900 +timestamp: 2024-12-20 21:23:59 +0900 pre-requisites: --output/tsv/ () ---prepare:ncbigene (2024-12-16 16:14:56 +0900) -latest-prerequisite time: 2024-12-16 16:14:56 +0900 +--prepare:ncbigene (2024-12-20 21:23:59 +0900) +latest-prerequisite time: 2024-12-20 21:23:59 +0900 ................................ -### Update TSV for ncit_disease-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for ncit_disease-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/ncit_disease-ncit_tissue.tsv is newer than config/ncit_disease-ncit_tissue/config.yaml # File output/tsv/ncit_disease-ncit_tissue.tsv has no timestamp file -# File output/tsv/ncit_disease-ncit_tissue.tsv is created 16.550975689469766 days ago (will be updated when >5 days) -## Update config/ncit_disease-ncit_tissue/config.yaml => output/tsv/ncit_disease-ncit_tissue.tsv -< 2024-12-16T16:14:56 ncit_disease-ncit_tissue -togoid-config config/ncit_disease-ncit_tissue update -# Success: output/tsv/ncit_disease-ncit_tissue.tsv is updated -> 2024-12-16T16:15:00 ncit_disease-ncit_tissue +# File output/tsv/ncit_disease-ncit_tissue.tsv is created 4.214566066648681 days ago (will be updated when >5 days) +# => Preserving output/tsv/ncit_disease-ncit_tissue.tsv Rule for TSV (output/tsv/ncit_disease-ncit_tissue.tsv) ------------------------------ Investigating output/tsv/ncit_disease-ncit_tissue.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:00 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for oma_protein-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -3338,8 +3272,8 @@ task needed: true timestamp: 2024-09-27 22:31:53 +0900 pre-requisites: --output/tsv/ () ---prepare:oma_protein (2024-12-16 16:15:00 +0900) -latest-prerequisite time: 2024-12-16 16:15:00 +0900 +--prepare:oma_protein (2024-12-20 21:23:59 +0900) +latest-prerequisite time: 2024-12-20 21:23:59 +0900 ................................ ### Update TSV for oma_protein-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -3354,8 +3288,8 @@ task needed: true timestamp: 2024-09-27 22:39:06 +0900 pre-requisites: --output/tsv/ () ---prepare:oma_protein (2024-12-16 16:15:00 +0900) -latest-prerequisite time: 2024-12-16 16:15:00 +0900 +--prepare:oma_protein (2024-12-20 21:23:59 +0900) +latest-prerequisite time: 2024-12-20 21:23:59 +0900 ................................ ### Update TSV for oma_protein-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -3370,8 +3304,8 @@ task needed: true timestamp: 2024-09-27 22:39:32 +0900 pre-requisites: --output/tsv/ () ---prepare:oma_protein (2024-12-16 16:15:00 +0900) -latest-prerequisite time: 2024-12-16 16:15:00 +0900 +--prepare:oma_protein (2024-12-20 21:23:59 +0900) +latest-prerequisite time: 2024-12-20 21:23:59 +0900 ................................ ### Update TSV for oma_protein-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -3386,301 +3320,249 @@ task needed: true timestamp: 2024-09-27 22:39:39 +0900 pre-requisites: --output/tsv/ () ---prepare:oma_protein (2024-12-16 16:15:00 +0900) -latest-prerequisite time: 2024-12-16 16:15:00 +0900 +--prepare:oma_protein (2024-12-20 21:23:59 +0900) +latest-prerequisite time: 2024-12-20 21:23:59 +0900 ................................ -### Update TSV for orphanet_gene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_gene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_gene-ensembl_gene.tsv is newer than config/orphanet_gene-ensembl_gene/config.yaml # File output/tsv/orphanet_gene-ensembl_gene.tsv has no timestamp file -# File output/tsv/orphanet_gene-ensembl_gene.tsv is created 9.785042958413136 days ago (will be updated when >5 days) -## Update config/orphanet_gene-ensembl_gene/config.yaml => output/tsv/orphanet_gene-ensembl_gene.tsv -< 2024-12-16T16:15:00 orphanet_gene-ensembl_gene -togoid-config config/orphanet_gene-ensembl_gene update -# Success: output/tsv/orphanet_gene-ensembl_gene.tsv is updated -> 2024-12-16T16:15:01 orphanet_gene-ensembl_gene +# File output/tsv/orphanet_gene-ensembl_gene.tsv is created 4.214561271255324 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_gene-ensembl_gene.tsv Rule for TSV (output/tsv/orphanet_gene-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/orphanet_gene-ensembl_gene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:01 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_gene-hgnc.tsv is newer than config/orphanet_gene-hgnc/config.yaml # File output/tsv/orphanet_gene-hgnc.tsv has no timestamp file -# File output/tsv/orphanet_gene-hgnc.tsv is created 9.785043001060846 days ago (will be updated when >5 days) -## Update config/orphanet_gene-hgnc/config.yaml => output/tsv/orphanet_gene-hgnc.tsv -< 2024-12-16T16:15:01 orphanet_gene-hgnc -togoid-config config/orphanet_gene-hgnc update -# Success: output/tsv/orphanet_gene-hgnc.tsv is updated -> 2024-12-16T16:15:01 orphanet_gene-hgnc +# File output/tsv/orphanet_gene-hgnc.tsv is created 4.214556450326701 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_gene-hgnc.tsv Rule for TSV (output/tsv/orphanet_gene-hgnc.tsv) ------------------------------ Investigating output/tsv/orphanet_gene-hgnc.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:01 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_gene-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_gene-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_gene-omim_gene.tsv is newer than config/orphanet_gene-omim_gene/config.yaml # File output/tsv/orphanet_gene-omim_gene.tsv has no timestamp file -# File output/tsv/orphanet_gene-omim_gene.tsv is created 9.785042942273044 days ago (will be updated when >5 days) -## Update config/orphanet_gene-omim_gene/config.yaml => output/tsv/orphanet_gene-omim_gene.tsv -< 2024-12-16T16:15:01 orphanet_gene-omim_gene -togoid-config config/orphanet_gene-omim_gene update -# Success: output/tsv/orphanet_gene-omim_gene.tsv is updated -> 2024-12-16T16:15:02 orphanet_gene-omim_gene +# File output/tsv/orphanet_gene-omim_gene.tsv is created 4.214551466713275 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_gene-omim_gene.tsv Rule for TSV (output/tsv/orphanet_gene-omim_gene.tsv) ------------------------------ Investigating output/tsv/orphanet_gene-omim_gene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_gene-uniprot.tsv is newer than config/orphanet_gene-uniprot/config.yaml # File output/tsv/orphanet_gene-uniprot.tsv has no timestamp file -# File output/tsv/orphanet_gene-uniprot.tsv is created 9.785043123819236 days ago (will be updated when >5 days) -## Update config/orphanet_gene-uniprot/config.yaml => output/tsv/orphanet_gene-uniprot.tsv -< 2024-12-16T16:15:02 orphanet_gene-uniprot -togoid-config config/orphanet_gene-uniprot update -# Success: output/tsv/orphanet_gene-uniprot.tsv is updated -> 2024-12-16T16:15:02 orphanet_gene-uniprot +# File output/tsv/orphanet_gene-uniprot.tsv is created 4.214546645196111 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_gene-uniprot.tsv Rule for TSV (output/tsv/orphanet_gene-uniprot.tsv) ------------------------------ Investigating output/tsv/orphanet_gene-uniprot.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_phenotype-meddra if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_phenotype-meddra if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_phenotype-meddra.tsv is newer than config/orphanet_phenotype-meddra/config.yaml # File output/tsv/orphanet_phenotype-meddra.tsv has no timestamp file -# File output/tsv/orphanet_phenotype-meddra.tsv is created 9.785043320526007 days ago (will be updated when >5 days) -## Update config/orphanet_phenotype-meddra/config.yaml => output/tsv/orphanet_phenotype-meddra.tsv -< 2024-12-16T16:15:02 orphanet_phenotype-meddra -togoid-config config/orphanet_phenotype-meddra update -# Success: output/tsv/orphanet_phenotype-meddra.tsv is updated -> 2024-12-16T16:15:02 orphanet_phenotype-meddra +# File output/tsv/orphanet_phenotype-meddra.tsv is created 4.214541927673217 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_phenotype-meddra.tsv Rule for TSV (output/tsv/orphanet_phenotype-meddra.tsv) ------------------------------ Investigating output/tsv/orphanet_phenotype-meddra.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:02 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_phenotype-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_phenotype-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_phenotype-mesh.tsv is newer than config/orphanet_phenotype-mesh/config.yaml # File output/tsv/orphanet_phenotype-mesh.tsv has no timestamp file -# File output/tsv/orphanet_phenotype-mesh.tsv is created 9.785043026956677 days ago (will be updated when >5 days) -## Update config/orphanet_phenotype-mesh/config.yaml => output/tsv/orphanet_phenotype-mesh.tsv -< 2024-12-16T16:15:02 orphanet_phenotype-mesh -togoid-config config/orphanet_phenotype-mesh update -# Success: output/tsv/orphanet_phenotype-mesh.tsv is updated -> 2024-12-16T16:15:03 orphanet_phenotype-mesh +# File output/tsv/orphanet_phenotype-mesh.tsv is created 4.214536640771991 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_phenotype-mesh.tsv Rule for TSV (output/tsv/orphanet_phenotype-mesh.tsv) ------------------------------ Investigating output/tsv/orphanet_phenotype-mesh.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:03 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_phenotype-omim_phenotype.tsv is newer than config/orphanet_phenotype-omim_phenotype/config.yaml # File output/tsv/orphanet_phenotype-omim_phenotype.tsv has no timestamp file -# File output/tsv/orphanet_phenotype-omim_phenotype.tsv is created 9.785043454561203 days ago (will be updated when >5 days) -## Update config/orphanet_phenotype-omim_phenotype/config.yaml => output/tsv/orphanet_phenotype-omim_phenotype.tsv -< 2024-12-16T16:15:03 orphanet_phenotype-omim_phenotype -togoid-config config/orphanet_phenotype-omim_phenotype update -# Success: output/tsv/orphanet_phenotype-omim_phenotype.tsv is updated -> 2024-12-16T16:15:03 orphanet_phenotype-omim_phenotype +# File output/tsv/orphanet_phenotype-omim_phenotype.tsv is created 4.214531415839606 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_phenotype-omim_phenotype.tsv Rule for TSV (output/tsv/orphanet_phenotype-omim_phenotype.tsv) ------------------------------ Investigating output/tsv/orphanet_phenotype-omim_phenotype.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:03 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for orphanet_phenotype-orphanet_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for orphanet_phenotype-orphanet_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/orphanet_phenotype-orphanet_gene.tsv is newer than config/orphanet_phenotype-orphanet_gene/config.yaml # File output/tsv/orphanet_phenotype-orphanet_gene.tsv has no timestamp file -# File output/tsv/orphanet_phenotype-orphanet_gene.tsv is created 9.785043071433275 days ago (will be updated when >5 days) -## Update config/orphanet_phenotype-orphanet_gene/config.yaml => output/tsv/orphanet_phenotype-orphanet_gene.tsv -< 2024-12-16T16:15:03 orphanet_phenotype-orphanet_gene -togoid-config config/orphanet_phenotype-orphanet_gene update -# Success: output/tsv/orphanet_phenotype-orphanet_gene.tsv is updated -> 2024-12-16T16:15:04 orphanet_phenotype-orphanet_gene +# File output/tsv/orphanet_phenotype-orphanet_gene.tsv is created 4.214526606448391 days ago (will be updated when >5 days) +# => Preserving output/tsv/orphanet_phenotype-orphanet_gene.tsv Rule for TSV (output/tsv/orphanet_phenotype-orphanet_gene.tsv) ------------------------------ Investigating output/tsv/orphanet_phenotype-orphanet_gene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:04 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pdb-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pdb-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pdb-go.tsv is newer than config/pdb-go/config.yaml # File output/tsv/pdb-go.tsv has no timestamp file -# File output/tsv/pdb-go.tsv is created 9.785001129799085 days ago (will be updated when >5 days) -## Update config/pdb-go/config.yaml => output/tsv/pdb-go.tsv -< 2024-12-16T16:15:04 pdb-go -togoid-config config/pdb-go update -# Success: output/tsv/pdb-go.tsv is updated -> 2024-12-16T16:15:08 pdb-go +# File output/tsv/pdb-go.tsv is created 4.214474794346574 days ago (will be updated when >5 days) +# => Preserving output/tsv/pdb-go.tsv Rule for TSV (output/tsv/pdb-go.tsv) ------------------------------ Investigating output/tsv/pdb-go.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:08 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pdb-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pdb-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pdb-interpro.tsv is newer than config/pdb-interpro/config.yaml # File output/tsv/pdb-interpro.tsv has no timestamp file -# File output/tsv/pdb-interpro.tsv is created 9.785035103822743 days ago (will be updated when >5 days) -## Update config/pdb-interpro/config.yaml => output/tsv/pdb-interpro.tsv -< 2024-12-16T16:15:08 pdb-interpro -togoid-config config/pdb-interpro update -# Success: output/tsv/pdb-interpro.tsv is updated -> 2024-12-16T16:15:10 pdb-interpro +# File output/tsv/pdb-interpro.tsv is created 4.214456604822824 days ago (will be updated when >5 days) +# => Preserving output/tsv/pdb-interpro.tsv Rule for TSV (output/tsv/pdb-interpro.tsv) ------------------------------ Investigating output/tsv/pdb-interpro.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pdb-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pdb-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pdb-pdb_ccd.tsv is newer than config/pdb-pdb_ccd/config.yaml # File output/tsv/pdb-pdb_ccd.tsv has no timestamp file -# File output/tsv/pdb-pdb_ccd.tsv is created 9.785040165801561 days ago (will be updated when >5 days) -## Update config/pdb-pdb_ccd/config.yaml => output/tsv/pdb-pdb_ccd.tsv -< 2024-12-16T16:15:10 pdb-pdb_ccd -togoid-config config/pdb-pdb_ccd update -# Success: output/tsv/pdb-pdb_ccd.tsv is updated -> 2024-12-16T16:15:11 pdb-pdb_ccd +# File output/tsv/pdb-pdb_ccd.tsv is created 4.2144431648051395 days ago (will be updated when >5 days) +# => Preserving output/tsv/pdb-pdb_ccd.tsv Rule for TSV (output/tsv/pdb-pdb_ccd.tsv) ------------------------------ Investigating output/tsv/pdb-pdb_ccd.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:11 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pdb-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pdb-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pdb-pfam.tsv is newer than config/pdb-pfam/config.yaml # File output/tsv/pdb-pfam.tsv has no timestamp file -# File output/tsv/pdb-pfam.tsv is created 9.785042305565694 days ago (will be updated when >5 days) -## Update config/pdb-pfam/config.yaml => output/tsv/pdb-pfam.tsv -< 2024-12-16T16:15:11 pdb-pfam -togoid-config config/pdb-pfam update -# Success: output/tsv/pdb-pfam.tsv is updated -> 2024-12-16T16:15:12 pdb-pfam +# File output/tsv/pdb-pfam.tsv is created 4.214432105269306 days ago (will be updated when >5 days) +# => Preserving output/tsv/pdb-pfam.tsv Rule for TSV (output/tsv/pdb-pfam.tsv) ------------------------------ Investigating output/tsv/pdb-pfam.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:12 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pdb-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pdb-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pdb-uniprot.tsv is newer than config/pdb-uniprot/config.yaml # File output/tsv/pdb-uniprot.tsv has no timestamp file -# File output/tsv/pdb-uniprot.tsv is created 9.785041545578773 days ago (will be updated when >5 days) -## Update config/pdb-uniprot/config.yaml => output/tsv/pdb-uniprot.tsv -< 2024-12-16T16:15:12 pdb-uniprot -togoid-config config/pdb-uniprot update -# Success: output/tsv/pdb-uniprot.tsv is updated -> 2024-12-16T16:15:13 pdb-uniprot +# File output/tsv/pdb-uniprot.tsv is created 4.214420478298311 days ago (will be updated when >5 days) +# => Preserving output/tsv/pdb-uniprot.tsv Rule for TSV (output/tsv/pdb-uniprot.tsv) ------------------------------ Investigating output/tsv/pdb-uniprot.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:15:13 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for pmc-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/pmc-pubmed.tsv is newer than config/pmc-pubmed/config.yaml # File output/tsv/pmc-pubmed.tsv is older than input/pmc/download.lock ## Update config/pmc-pubmed/config.yaml => output/tsv/pmc-pubmed.tsv -< 2024-12-16T16:15:13 pmc-pubmed +< 2024-12-20T21:23:59 pmc-pubmed togoid-config config/pmc-pubmed update # Success: output/tsv/pmc-pubmed.tsv is updated -> 2024-12-16T16:21:00 pmc-pubmed +> 2024-12-20T21:29:50 pmc-pubmed Rule for TSV (output/tsv/pmc-pubmed.tsv) ------------------------------ Investigating output/tsv/pmc-pubmed.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:21:00 +0900 +timestamp: 2024-12-20 21:29:50 +0900 pre-requisites: --output/tsv/ () ---prepare:pmc (2024-12-16 16:21:00 +0900) -latest-prerequisite time: 2024-12-16 16:21:00 +0900 +--prepare:pmc (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ ### Update TSV for prosite-prosite_prorule if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -3695,271 +3577,219 @@ task needed: true timestamp: 2024-11-30 03:07:42 +0900 pre-requisites: --output/tsv/ () ---prepare:prosite (2024-12-16 16:21:00 +0900) -latest-prerequisite time: 2024-12-16 16:21:00 +0900 +--prepare:prosite (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for pubchem_compound-atc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-atc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-atc.tsv is newer than config/pubchem_compound-atc/config.yaml # File output/tsv/pubchem_compound-atc.tsv has no timestamp file -# File output/tsv/pubchem_compound-atc.tsv is created 9.785023232905347 days ago (will be updated when >5 days) -## Update config/pubchem_compound-atc/config.yaml => output/tsv/pubchem_compound-atc.tsv -< 2024-12-16T16:21:00 pubchem_compound-atc -togoid-config config/pubchem_compound-atc update -# Success: output/tsv/pubchem_compound-atc.tsv is updated -> 2024-12-16T16:21:00 pubchem_compound-atc +# File output/tsv/pubchem_compound-atc.tsv is created 4.214471770777094 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-atc.tsv Rule for TSV (output/tsv/pubchem_compound-atc.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-atc.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:21:00 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-chebi.tsv is newer than config/pubchem_compound-chebi/config.yaml # File output/tsv/pubchem_compound-chebi.tsv has no timestamp file -# File output/tsv/pubchem_compound-chebi.tsv is created 9.78501968147088 days ago (will be updated when >5 days) -## Update config/pubchem_compound-chebi/config.yaml => output/tsv/pubchem_compound-chebi.tsv -< 2024-12-16T16:21:00 pubchem_compound-chebi -togoid-config config/pubchem_compound-chebi update -# Success: output/tsv/pubchem_compound-chebi.tsv is updated -> 2024-12-16T16:21:01 pubchem_compound-chebi +# File output/tsv/pubchem_compound-chebi.tsv is created 4.21446345458728 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-chebi.tsv Rule for TSV (output/tsv/pubchem_compound-chebi.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-chebi.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:21:01 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_compound-chembl_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-chembl_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-chembl_compound.tsv is newer than config/pubchem_compound-chembl_compound/config.yaml # File output/tsv/pubchem_compound-chembl_compound.tsv has no timestamp file -# File output/tsv/pubchem_compound-chembl_compound.tsv is created 9.78497103901817 days ago (will be updated when >5 days) -## Update config/pubchem_compound-chembl_compound/config.yaml => output/tsv/pubchem_compound-chembl_compound.tsv -< 2024-12-16T16:21:01 pubchem_compound-chembl_compound -togoid-config config/pubchem_compound-chembl_compound update -# Success: output/tsv/pubchem_compound-chembl_compound.tsv is updated -> 2024-12-16T16:21:06 pubchem_compound-chembl_compound +# File output/tsv/pubchem_compound-chembl_compound.tsv is created 4.214407498727407 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-chembl_compound.tsv Rule for TSV (output/tsv/pubchem_compound-chembl_compound.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-chembl_compound.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:21:06 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-drugbank.tsv is newer than config/pubchem_compound-drugbank/config.yaml # File output/tsv/pubchem_compound-drugbank.tsv has no timestamp file -# File output/tsv/pubchem_compound-drugbank.tsv is created 9.785022527569884 days ago (will be updated when >5 days) -## Update config/pubchem_compound-drugbank/config.yaml => output/tsv/pubchem_compound-drugbank.tsv -< 2024-12-16T16:21:06 pubchem_compound-drugbank -togoid-config config/pubchem_compound-drugbank update -# Success: output/tsv/pubchem_compound-drugbank.tsv is updated -> 2024-12-16T16:21:06 pubchem_compound-drugbank +# File output/tsv/pubchem_compound-drugbank.tsv is created 4.214402539040046 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-drugbank.tsv Rule for TSV (output/tsv/pubchem_compound-drugbank.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-drugbank.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:21:06 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_compound-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-glytoucan.tsv is newer than config/pubchem_compound-glytoucan/config.yaml # File output/tsv/pubchem_compound-glytoucan.tsv has no timestamp file -# File output/tsv/pubchem_compound-glytoucan.tsv is created 9.785021618500418 days ago (will be updated when >5 days) -## Update config/pubchem_compound-glytoucan/config.yaml => output/tsv/pubchem_compound-glytoucan.tsv -< 2024-12-16T16:21:06 pubchem_compound-glytoucan -togoid-config config/pubchem_compound-glytoucan update -# Success: output/tsv/pubchem_compound-glytoucan.tsv is updated -> 2024-12-16T16:21:07 pubchem_compound-glytoucan +# File output/tsv/pubchem_compound-glytoucan.tsv is created 4.214396213142291 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-glytoucan.tsv Rule for TSV (output/tsv/pubchem_compound-glytoucan.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-glytoucan.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:21:07 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_compound-inchi_key.tsv is newer than config/pubchem_compound-inchi_key/config.yaml # File output/tsv/pubchem_compound-inchi_key.tsv has no timestamp file -# File output/tsv/pubchem_compound-inchi_key.tsv is created 9.778751035899445 days ago (will be updated when >5 days) -## Update config/pubchem_compound-inchi_key/config.yaml => output/tsv/pubchem_compound-inchi_key.tsv -< 2024-12-16T16:21:07 pubchem_compound-inchi_key -togoid-config config/pubchem_compound-inchi_key update -# Success: output/tsv/pubchem_compound-inchi_key.tsv is updated -> 2024-12-16T16:27:49 pubchem_compound-inchi_key +# File output/tsv/pubchem_compound-inchi_key.tsv is created 4.209744095589884 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_compound-inchi_key.tsv Rule for TSV (output/tsv/pubchem_compound-inchi_key.tsv) ------------------------------ Investigating output/tsv/pubchem_compound-inchi_key.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:49 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-ncbigene.tsv is newer than config/pubchem_pathway-ncbigene/config.yaml # File output/tsv/pubchem_pathway-ncbigene.tsv has no timestamp file -# File output/tsv/pubchem_pathway-ncbigene.tsv is created 9.783396074745314 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-ncbigene/config.yaml => output/tsv/pubchem_pathway-ncbigene.tsv -< 2024-12-16T16:27:49 pubchem_pathway-ncbigene -togoid-config config/pubchem_pathway-ncbigene update -# Success: output/tsv/pubchem_pathway-ncbigene.tsv is updated -> 2024-12-16T16:27:49 pubchem_pathway-ncbigene +# File output/tsv/pubchem_pathway-ncbigene.tsv is created 4.2097383484898385 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-ncbigene.tsv Rule for TSV (output/tsv/pubchem_pathway-ncbigene.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-ncbigene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:49 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-pathbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-pathbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-pathbank.tsv is newer than config/pubchem_pathway-pathbank/config.yaml # File output/tsv/pubchem_pathway-pathbank.tsv has no timestamp file -# File output/tsv/pubchem_pathway-pathbank.tsv is created 9.783395808169919 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-pathbank/config.yaml => output/tsv/pubchem_pathway-pathbank.tsv -< 2024-12-16T16:27:49 pubchem_pathway-pathbank -togoid-config config/pubchem_pathway-pathbank update -# Success: output/tsv/pubchem_pathway-pathbank.tsv is updated -> 2024-12-16T16:27:50 pubchem_pathway-pathbank +# File output/tsv/pubchem_pathway-pathbank.tsv is created 4.2097321964120376 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-pathbank.tsv Rule for TSV (output/tsv/pubchem_pathway-pathbank.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-pathbank.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:50 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-pubchem_compound.tsv is newer than config/pubchem_pathway-pubchem_compound/config.yaml # File output/tsv/pubchem_pathway-pubchem_compound.tsv has no timestamp file -# File output/tsv/pubchem_pathway-pubchem_compound.tsv is created 9.783370552293922 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-pubchem_compound/config.yaml => output/tsv/pubchem_pathway-pubchem_compound.tsv -< 2024-12-16T16:27:50 pubchem_pathway-pubchem_compound -togoid-config config/pubchem_pathway-pubchem_compound update -# Success: output/tsv/pubchem_pathway-pubchem_compound.tsv is updated -> 2024-12-16T16:27:52 pubchem_pathway-pubchem_compound +# File output/tsv/pubchem_pathway-pubchem_compound.tsv is created 4.209702918865833 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-pubchem_compound.tsv Rule for TSV (output/tsv/pubchem_pathway-pubchem_compound.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-pubchem_compound.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:52 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-reactome_pathway.tsv is newer than config/pubchem_pathway-reactome_pathway/config.yaml # File output/tsv/pubchem_pathway-reactome_pathway.tsv has no timestamp file -# File output/tsv/pubchem_pathway-reactome_pathway.tsv is created 9.783395438081413 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-reactome_pathway/config.yaml => output/tsv/pubchem_pathway-reactome_pathway.tsv -< 2024-12-16T16:27:52 pubchem_pathway-reactome_pathway -togoid-config config/pubchem_pathway-reactome_pathway update -# Success: output/tsv/pubchem_pathway-reactome_pathway.tsv is updated -> 2024-12-16T16:27:53 pubchem_pathway-reactome_pathway +# File output/tsv/pubchem_pathway-reactome_pathway.tsv is created 4.209698384113159 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-reactome_pathway.tsv Rule for TSV (output/tsv/pubchem_pathway-reactome_pathway.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-reactome_pathway.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:52 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-uniprot.tsv is newer than config/pubchem_pathway-uniprot/config.yaml # File output/tsv/pubchem_pathway-uniprot.tsv has no timestamp file -# File output/tsv/pubchem_pathway-uniprot.tsv is created 9.783383135179804 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-uniprot/config.yaml => output/tsv/pubchem_pathway-uniprot.tsv -< 2024-12-16T16:27:53 pubchem_pathway-uniprot -togoid-config config/pubchem_pathway-uniprot update -# Success: output/tsv/pubchem_pathway-uniprot.tsv is updated -> 2024-12-16T16:27:54 pubchem_pathway-uniprot +# File output/tsv/pubchem_pathway-uniprot.tsv is created 4.209680774777928 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-uniprot.tsv Rule for TSV (output/tsv/pubchem_pathway-uniprot.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-uniprot.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:54 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for pubchem_pathway-wikipathways if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for pubchem_pathway-wikipathways if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/pubchem_pathway-wikipathways.tsv is newer than config/pubchem_pathway-wikipathways/config.yaml # File output/tsv/pubchem_pathway-wikipathways.tsv has no timestamp file -# File output/tsv/pubchem_pathway-wikipathways.tsv is created 9.783396559558842 days ago (will be updated when >5 days) -## Update config/pubchem_pathway-wikipathways/config.yaml => output/tsv/pubchem_pathway-wikipathways.tsv -< 2024-12-16T16:27:54 pubchem_pathway-wikipathways -togoid-config config/pubchem_pathway-wikipathways update -# Success: output/tsv/pubchem_pathway-wikipathways.tsv is updated -> 2024-12-16T16:27:54 pubchem_pathway-wikipathways +# File output/tsv/pubchem_pathway-wikipathways.tsv is created 4.209676186923958 days ago (will be updated when >5 days) +# => Preserving output/tsv/pubchem_pathway-wikipathways.tsv Rule for TSV (output/tsv/pubchem_pathway-wikipathways.tsv) ------------------------------ Investigating output/tsv/pubchem_pathway-wikipathways.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 16:27:54 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for reactome_pathway-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-chebi.tsv is newer than config/reactome_pathway-chebi/config.yaml # File output/tsv/reactome_pathway-chebi.tsv has no timestamp file -# File output/tsv/reactome_pathway-chebi.tsv is created 9.783394936231366 days ago (will be updated when >5 days) -## Update config/reactome_pathway-chebi/config.yaml => output/tsv/reactome_pathway-chebi.tsv -< 2024-12-16T16:27:54 reactome_pathway-chebi -togoid-config config/reactome_pathway-chebi update -# Success: output/tsv/reactome_pathway-chebi.tsv is updated -> 2024-12-16T16:27:55 reactome_pathway-chebi +# File output/tsv/reactome_pathway-chebi.tsv is created 4.209669122324838 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-chebi.tsv Rule for TSV (output/tsv/reactome_pathway-chebi.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-chebi.tsv @@ -3968,19 +3798,15 @@ task needed: true timestamp: 2024-12-16 16:27:55 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:55 +0900) -latest-prerequisite time: 2024-12-16 16:27:55 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_pathway-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-go.tsv is newer than config/reactome_pathway-go/config.yaml # File output/tsv/reactome_pathway-go.tsv has no timestamp file -# File output/tsv/reactome_pathway-go.tsv is created 9.783396869989074 days ago (will be updated when >5 days) -## Update config/reactome_pathway-go/config.yaml => output/tsv/reactome_pathway-go.tsv -< 2024-12-16T16:27:55 reactome_pathway-go -togoid-config config/reactome_pathway-go update -# Success: output/tsv/reactome_pathway-go.tsv is updated -> 2024-12-16T16:27:55 reactome_pathway-go +# File output/tsv/reactome_pathway-go.tsv is created 4.209664000940706 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-go.tsv Rule for TSV (output/tsv/reactome_pathway-go.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-go.tsv @@ -3989,19 +3815,15 @@ task needed: true timestamp: 2024-12-16 16:27:55 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:55 +0900) -latest-prerequisite time: 2024-12-16 16:27:55 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_pathway-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-iuphar_ligand.tsv is newer than config/reactome_pathway-iuphar_ligand/config.yaml # File output/tsv/reactome_pathway-iuphar_ligand.tsv has no timestamp file -# File output/tsv/reactome_pathway-iuphar_ligand.tsv is created 9.783398029319745 days ago (will be updated when >5 days) -## Update config/reactome_pathway-iuphar_ligand/config.yaml => output/tsv/reactome_pathway-iuphar_ligand.tsv -< 2024-12-16T16:27:55 reactome_pathway-iuphar_ligand -togoid-config config/reactome_pathway-iuphar_ligand update -# Success: output/tsv/reactome_pathway-iuphar_ligand.tsv is updated -> 2024-12-16T16:27:56 reactome_pathway-iuphar_ligand +# File output/tsv/reactome_pathway-iuphar_ligand.tsv is created 4.20966048803625 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-iuphar_ligand.tsv Rule for TSV (output/tsv/reactome_pathway-iuphar_ligand.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-iuphar_ligand.tsv @@ -4010,19 +3832,15 @@ task needed: true timestamp: 2024-12-16 16:27:56 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:56 +0900) -latest-prerequisite time: 2024-12-16 16:27:56 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_pathway-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-mirbase.tsv is newer than config/reactome_pathway-mirbase/config.yaml # File output/tsv/reactome_pathway-mirbase.tsv has no timestamp file -# File output/tsv/reactome_pathway-mirbase.tsv is created 9.783399076159316 days ago (will be updated when >5 days) -## Update config/reactome_pathway-mirbase/config.yaml => output/tsv/reactome_pathway-mirbase.tsv -< 2024-12-16T16:27:56 reactome_pathway-mirbase -togoid-config config/reactome_pathway-mirbase update -# Success: output/tsv/reactome_pathway-mirbase.tsv is updated -> 2024-12-16T16:27:56 reactome_pathway-mirbase +# File output/tsv/reactome_pathway-mirbase.tsv is created 4.209657854766539 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-mirbase.tsv Rule for TSV (output/tsv/reactome_pathway-mirbase.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-mirbase.tsv @@ -4031,19 +3849,15 @@ task needed: true timestamp: 2024-12-16 16:27:56 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:56 +0900) -latest-prerequisite time: 2024-12-16 16:27:56 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_pathway-reactome_reaction if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-reactome_reaction if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-reactome_reaction.tsv is newer than config/reactome_pathway-reactome_reaction/config.yaml # File output/tsv/reactome_pathway-reactome_reaction.tsv has no timestamp file -# File output/tsv/reactome_pathway-reactome_reaction.tsv is created 9.783388487202535 days ago (will be updated when >5 days) -## Update config/reactome_pathway-reactome_reaction/config.yaml => output/tsv/reactome_pathway-reactome_reaction.tsv -< 2024-12-16T16:27:56 reactome_pathway-reactome_reaction -togoid-config config/reactome_pathway-reactome_reaction update -# Success: output/tsv/reactome_pathway-reactome_reaction.tsv is updated -> 2024-12-16T16:27:57 reactome_pathway-reactome_reaction +# File output/tsv/reactome_pathway-reactome_reaction.tsv is created 4.209644762673623 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-reactome_reaction.tsv Rule for TSV (output/tsv/reactome_pathway-reactome_reaction.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-reactome_reaction.tsv @@ -4052,19 +3866,15 @@ task needed: true timestamp: 2024-12-16 16:27:57 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:57 +0900) -latest-prerequisite time: 2024-12-16 16:27:57 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_pathway-uniprot.tsv is newer than config/reactome_pathway-uniprot/config.yaml # File output/tsv/reactome_pathway-uniprot.tsv has no timestamp file -# File output/tsv/reactome_pathway-uniprot.tsv is created 9.783386700597662 days ago (will be updated when >5 days) -## Update config/reactome_pathway-uniprot/config.yaml => output/tsv/reactome_pathway-uniprot.tsv -< 2024-12-16T16:27:57 reactome_pathway-uniprot -togoid-config config/reactome_pathway-uniprot update -# Success: output/tsv/reactome_pathway-uniprot.tsv is updated -> 2024-12-16T16:27:58 reactome_pathway-uniprot +# File output/tsv/reactome_pathway-uniprot.tsv is created 4.2096308911835765 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_pathway-uniprot.tsv Rule for TSV (output/tsv/reactome_pathway-uniprot.tsv) ------------------------------ Investigating output/tsv/reactome_pathway-uniprot.tsv @@ -4073,19 +3883,15 @@ task needed: true timestamp: 2024-12-16 16:27:58 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:58 +0900) -latest-prerequisite time: 2024-12-16 16:27:58 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_reaction-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_reaction-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_reaction-chebi.tsv is newer than config/reactome_reaction-chebi/config.yaml # File output/tsv/reactome_reaction-chebi.tsv has no timestamp file -# File output/tsv/reactome_reaction-chebi.tsv is created 9.783395571937257 days ago (will be updated when >5 days) -## Update config/reactome_reaction-chebi/config.yaml => output/tsv/reactome_reaction-chebi.tsv -< 2024-12-16T16:27:58 reactome_reaction-chebi -togoid-config config/reactome_reaction-chebi update -# Success: output/tsv/reactome_reaction-chebi.tsv is updated -> 2024-12-16T16:27:59 reactome_reaction-chebi +# File output/tsv/reactome_reaction-chebi.tsv is created 4.209624739460405 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_reaction-chebi.tsv Rule for TSV (output/tsv/reactome_reaction-chebi.tsv) ------------------------------ Investigating output/tsv/reactome_reaction-chebi.tsv @@ -4094,19 +3900,15 @@ task needed: true timestamp: 2024-12-16 16:27:59 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:59 +0900) -latest-prerequisite time: 2024-12-16 16:27:59 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_reaction-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_reaction-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_reaction-go.tsv is newer than config/reactome_reaction-go/config.yaml # File output/tsv/reactome_reaction-go.tsv has no timestamp file -# File output/tsv/reactome_reaction-go.tsv is created 9.783396867801134 days ago (will be updated when >5 days) -## Update config/reactome_reaction-go/config.yaml => output/tsv/reactome_reaction-go.tsv -< 2024-12-16T16:27:59 reactome_reaction-go -togoid-config config/reactome_reaction-go update -# Success: output/tsv/reactome_reaction-go.tsv is updated -> 2024-12-16T16:27:59 reactome_reaction-go +# File output/tsv/reactome_reaction-go.tsv is created 4.209620612981956 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_reaction-go.tsv Rule for TSV (output/tsv/reactome_reaction-go.tsv) ------------------------------ Investigating output/tsv/reactome_reaction-go.tsv @@ -4115,19 +3917,15 @@ task needed: true timestamp: 2024-12-16 16:27:59 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:27:59 +0900) -latest-prerequisite time: 2024-12-16 16:27:59 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_reaction-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_reaction-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_reaction-iuphar_ligand.tsv is newer than config/reactome_reaction-iuphar_ligand/config.yaml # File output/tsv/reactome_reaction-iuphar_ligand.tsv has no timestamp file -# File output/tsv/reactome_reaction-iuphar_ligand.tsv is created 9.783397784736412 days ago (will be updated when >5 days) -## Update config/reactome_reaction-iuphar_ligand/config.yaml => output/tsv/reactome_reaction-iuphar_ligand.tsv -< 2024-12-16T16:27:59 reactome_reaction-iuphar_ligand -togoid-config config/reactome_reaction-iuphar_ligand update -# Success: output/tsv/reactome_reaction-iuphar_ligand.tsv is updated -> 2024-12-16T16:28:00 reactome_reaction-iuphar_ligand +# File output/tsv/reactome_reaction-iuphar_ligand.tsv is created 4.209617308404641 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_reaction-iuphar_ligand.tsv Rule for TSV (output/tsv/reactome_reaction-iuphar_ligand.tsv) ------------------------------ Investigating output/tsv/reactome_reaction-iuphar_ligand.tsv @@ -4136,19 +3934,15 @@ task needed: true timestamp: 2024-12-16 16:28:00 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:28:00 +0900) -latest-prerequisite time: 2024-12-16 16:28:00 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_reaction-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_reaction-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_reaction-mirbase.tsv is newer than config/reactome_reaction-mirbase/config.yaml # File output/tsv/reactome_reaction-mirbase.tsv has no timestamp file -# File output/tsv/reactome_reaction-mirbase.tsv is created 9.783398476937661 days ago (will be updated when >5 days) -## Update config/reactome_reaction-mirbase/config.yaml => output/tsv/reactome_reaction-mirbase.tsv -< 2024-12-16T16:28:00 reactome_reaction-mirbase -togoid-config config/reactome_reaction-mirbase update -# Success: output/tsv/reactome_reaction-mirbase.tsv is updated -> 2024-12-16T16:28:00 reactome_reaction-mirbase +# File output/tsv/reactome_reaction-mirbase.tsv is created 4.2096145593592595 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_reaction-mirbase.tsv Rule for TSV (output/tsv/reactome_reaction-mirbase.tsv) ------------------------------ Investigating output/tsv/reactome_reaction-mirbase.tsv @@ -4157,19 +3951,15 @@ task needed: true timestamp: 2024-12-16 16:28:00 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:28:00 +0900) -latest-prerequisite time: 2024-12-16 16:28:00 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ -### Update TSV for reactome_reaction-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for reactome_reaction-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/reactome_reaction-uniprot.tsv is newer than config/reactome_reaction-uniprot/config.yaml # File output/tsv/reactome_reaction-uniprot.tsv has no timestamp file -# File output/tsv/reactome_reaction-uniprot.tsv is created 9.783388201758807 days ago (will be updated when >5 days) -## Update config/reactome_reaction-uniprot/config.yaml => output/tsv/reactome_reaction-uniprot.tsv -< 2024-12-16T16:28:00 reactome_reaction-uniprot -togoid-config config/reactome_reaction-uniprot update -# Success: output/tsv/reactome_reaction-uniprot.tsv is updated -> 2024-12-16T16:28:01 reactome_reaction-uniprot +# File output/tsv/reactome_reaction-uniprot.tsv is created 4.209601208296412 days ago (will be updated when >5 days) +# => Preserving output/tsv/reactome_reaction-uniprot.tsv Rule for TSV (output/tsv/reactome_reaction-uniprot.tsv) ------------------------------ Investigating output/tsv/reactome_reaction-uniprot.tsv @@ -4178,28 +3968,28 @@ task needed: true timestamp: 2024-12-16 16:28:01 +0900 pre-requisites: --output/tsv/ () ---prepare:reactome (2024-12-16 16:28:01 +0900) -latest-prerequisite time: 2024-12-16 16:28:01 +0900 +--prepare:reactome (2024-12-20 21:29:50 +0900) +latest-prerequisite time: 2024-12-20 21:29:50 +0900 ................................ ### Update TSV for refseq_protein-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/refseq_protein-uniprot.tsv is newer than config/refseq_protein-uniprot/config.yaml # File output/tsv/refseq_protein-uniprot.tsv is older than input/refseq_protein/download.lock ## Update config/refseq_protein-uniprot/config.yaml => output/tsv/refseq_protein-uniprot.tsv -< 2024-12-16T16:28:01 refseq_protein-uniprot +< 2024-12-20T21:29:50 refseq_protein-uniprot togoid-config config/refseq_protein-uniprot update # Success: output/tsv/refseq_protein-uniprot.tsv is updated -> 2024-12-16T16:35:33 refseq_protein-uniprot +> 2024-12-20T21:36:47 refseq_protein-uniprot Rule for TSV (output/tsv/refseq_protein-uniprot.tsv) ------------------------------ Investigating output/tsv/refseq_protein-uniprot.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 16:35:33 +0900 +timestamp: 2024-12-20 21:36:47 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_protein (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_protein (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4214,8 +4004,8 @@ task needed: true timestamp: 2024-11-16 05:24:22 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4230,8 +4020,8 @@ task needed: true timestamp: 2024-11-16 05:27:15 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4246,8 +4036,8 @@ task needed: true timestamp: 2024-11-16 05:31:03 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4262,8 +4052,8 @@ task needed: true timestamp: 2024-11-16 05:32:50 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4278,8 +4068,8 @@ task needed: true timestamp: 2024-11-16 05:34:56 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4294,8 +4084,8 @@ task needed: true timestamp: 2024-11-16 05:38:35 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for refseq_rna-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4310,8 +4100,8 @@ task needed: true timestamp: 2024-11-16 05:41:38 +0900 pre-requisites: --output/tsv/ () ---prepare:refseq_rna (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:refseq_rna (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4326,8 +4116,8 @@ task needed: true timestamp: 2024-11-30 03:21:57 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4342,8 +4132,8 @@ task needed: true timestamp: 2024-11-30 03:21:58 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4358,8 +4148,8 @@ task needed: true timestamp: 2024-11-30 03:21:58 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4374,8 +4164,8 @@ task needed: true timestamp: 2024-11-30 03:21:58 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-reactome_reaction if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4390,8 +4180,8 @@ task needed: true timestamp: 2024-11-30 03:21:59 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for rhea-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -4406,19 +4196,15 @@ task needed: true timestamp: 2024-11-30 03:22:39 +0900 pre-requisites: --output/tsv/ () ---prepare:rhea (2024-12-16 16:35:33 +0900) -latest-prerequisite time: 2024-12-16 16:35:33 +0900 +--prepare:rhea (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-bioproject.tsv is newer than config/sra_accession-bioproject/config.yaml # File output/tsv/sra_accession-bioproject.tsv has no timestamp file -# File output/tsv/sra_accession-bioproject.tsv is created 9.782851199862048 days ago (will be updated when >5 days) -## Update config/sra_accession-bioproject/config.yaml => output/tsv/sra_accession-bioproject.tsv -< 2024-12-16T16:35:33 sra_accession-bioproject -togoid-config config/sra_accession-bioproject update -# Success: output/tsv/sra_accession-bioproject.tsv is updated -> 2024-12-16T16:36:55 sra_accession-bioproject +# File output/tsv/sra_accession-bioproject.tsv is created 4.208247640864016 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-bioproject.tsv Rule for TSV (output/tsv/sra_accession-bioproject.tsv) ------------------------------ Investigating output/tsv/sra_accession-bioproject.tsv @@ -4427,19 +4213,15 @@ task needed: true timestamp: 2024-12-16 16:36:55 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 16:36:55 +0900) -latest-prerequisite time: 2024-12-16 16:36:55 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-biosample.tsv is newer than config/sra_accession-biosample/config.yaml # File output/tsv/sra_accession-biosample.tsv has no timestamp file -# File output/tsv/sra_accession-biosample.tsv is created 9.777913454370568 days ago (will be updated when >5 days) -## Update config/sra_accession-biosample/config.yaml => output/tsv/sra_accession-biosample.tsv -< 2024-12-16T16:36:55 sra_accession-biosample -togoid-config config/sra_accession-biosample update -# Success: output/tsv/sra_accession-biosample.tsv is updated -> 2024-12-16T16:45:25 sra_accession-biosample +# File output/tsv/sra_accession-biosample.tsv is created 4.202342083524814 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-biosample.tsv Rule for TSV (output/tsv/sra_accession-biosample.tsv) ------------------------------ Investigating output/tsv/sra_accession-biosample.tsv @@ -4448,19 +4230,15 @@ task needed: true timestamp: 2024-12-16 16:45:25 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 16:45:25 +0900) -latest-prerequisite time: 2024-12-16 16:45:25 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-sra_analysis if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-sra_analysis if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-sra_analysis.tsv is newer than config/sra_accession-sra_analysis/config.yaml # File output/tsv/sra_accession-sra_analysis.tsv has no timestamp file -# File output/tsv/sra_accession-sra_analysis.tsv is created 9.783006902278878 days ago (will be updated when >5 days) -## Update config/sra_accession-sra_analysis/config.yaml => output/tsv/sra_accession-sra_analysis.tsv -< 2024-12-16T16:45:25 sra_accession-sra_analysis -togoid-config config/sra_accession-sra_analysis update -# Success: output/tsv/sra_accession-sra_analysis.tsv is updated -> 2024-12-16T16:46:35 sra_accession-sra_analysis +# File output/tsv/sra_accession-sra_analysis.tsv is created 4.201526851185845 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-sra_analysis.tsv Rule for TSV (output/tsv/sra_accession-sra_analysis.tsv) ------------------------------ Investigating output/tsv/sra_accession-sra_analysis.tsv @@ -4469,19 +4247,15 @@ task needed: true timestamp: 2024-12-16 16:46:35 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 16:46:35 +0900) -latest-prerequisite time: 2024-12-16 16:46:35 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-sra_experiment.tsv is newer than config/sra_accession-sra_experiment/config.yaml # File output/tsv/sra_accession-sra_experiment.tsv has no timestamp file -# File output/tsv/sra_accession-sra_experiment.tsv is created 9.778981371432478 days ago (will be updated when >5 days) -## Update config/sra_accession-sra_experiment/config.yaml => output/tsv/sra_accession-sra_experiment.tsv -< 2024-12-16T16:46:35 sra_accession-sra_experiment -togoid-config config/sra_accession-sra_experiment update -# Success: output/tsv/sra_accession-sra_experiment.tsv is updated -> 2024-12-16T16:53:42 sra_accession-sra_experiment +# File output/tsv/sra_accession-sra_experiment.tsv is created 4.196583003592581 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-sra_experiment.tsv Rule for TSV (output/tsv/sra_accession-sra_experiment.tsv) ------------------------------ Investigating output/tsv/sra_accession-sra_experiment.tsv @@ -4490,19 +4264,15 @@ task needed: true timestamp: 2024-12-16 16:53:42 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 16:53:42 +0900) -latest-prerequisite time: 2024-12-16 16:53:42 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-sra_project.tsv is newer than config/sra_accession-sra_project/config.yaml # File output/tsv/sra_accession-sra_project.tsv has no timestamp file -# File output/tsv/sra_accession-sra_project.tsv is created 9.783131375658959 days ago (will be updated when >5 days) -## Update config/sra_accession-sra_project/config.yaml => output/tsv/sra_accession-sra_project.tsv -< 2024-12-16T16:53:42 sra_accession-sra_project -togoid-config config/sra_accession-sra_project update -# Success: output/tsv/sra_accession-sra_project.tsv is updated -> 2024-12-16T16:54:52 sra_accession-sra_project +# File output/tsv/sra_accession-sra_project.tsv is created 4.1957786977889935 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-sra_project.tsv Rule for TSV (output/tsv/sra_accession-sra_project.tsv) ------------------------------ Investigating output/tsv/sra_accession-sra_project.tsv @@ -4511,19 +4281,15 @@ task needed: true timestamp: 2024-12-16 16:54:52 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 16:54:52 +0900) -latest-prerequisite time: 2024-12-16 16:54:52 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-sra_run if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-sra_run if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-sra_run.tsv is newer than config/sra_accession-sra_run/config.yaml # File output/tsv/sra_accession-sra_run.tsv has no timestamp file -# File output/tsv/sra_accession-sra_run.tsv is created 9.778301798497766 days ago (will be updated when >5 days) -## Update config/sra_accession-sra_run/config.yaml => output/tsv/sra_accession-sra_run.tsv -< 2024-12-16T16:54:52 sra_accession-sra_run -togoid-config config/sra_accession-sra_run update -# Success: output/tsv/sra_accession-sra_run.tsv is updated -> 2024-12-16T17:02:48 sra_accession-sra_run +# File output/tsv/sra_accession-sra_run.tsv is created 4.190267738262685 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-sra_run.tsv Rule for TSV (output/tsv/sra_accession-sra_run.tsv) ------------------------------ Investigating output/tsv/sra_accession-sra_run.tsv @@ -4532,19 +4298,15 @@ task needed: true timestamp: 2024-12-16 17:02:48 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:02:48 +0900) -latest-prerequisite time: 2024-12-16 17:02:48 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_accession-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_accession-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_accession-sra_sample.tsv is newer than config/sra_accession-sra_sample/config.yaml # File output/tsv/sra_accession-sra_sample.tsv has no timestamp file -# File output/tsv/sra_accession-sra_sample.tsv is created 9.77903757159148 days ago (will be updated when >5 days) -## Update config/sra_accession-sra_sample/config.yaml => output/tsv/sra_accession-sra_sample.tsv -< 2024-12-16T17:02:48 sra_accession-sra_sample -togoid-config config/sra_accession-sra_sample update -# Success: output/tsv/sra_accession-sra_sample.tsv is updated -> 2024-12-16T17:09:41 sra_accession-sra_sample +# File output/tsv/sra_accession-sra_sample.tsv is created 4.185493751485324 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_accession-sra_sample.tsv Rule for TSV (output/tsv/sra_accession-sra_sample.tsv) ------------------------------ Investigating output/tsv/sra_accession-sra_sample.tsv @@ -4553,19 +4315,15 @@ task needed: true timestamp: 2024-12-16 17:09:41 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:09:41 +0900) -latest-prerequisite time: 2024-12-16 17:09:41 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_experiment-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_experiment-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_experiment-bioproject.tsv is newer than config/sra_experiment-bioproject/config.yaml # File output/tsv/sra_experiment-bioproject.tsv has no timestamp file -# File output/tsv/sra_experiment-bioproject.tsv is created 9.78126227206845 days ago (will be updated when >5 days) -## Update config/sra_experiment-bioproject/config.yaml => output/tsv/sra_experiment-bioproject.tsv -< 2024-12-16T17:09:41 sra_experiment-bioproject -togoid-config config/sra_experiment-bioproject update -# Success: output/tsv/sra_experiment-bioproject.tsv is updated -> 2024-12-16T17:13:23 sra_experiment-bioproject +# File output/tsv/sra_experiment-bioproject.tsv is created 4.182923715230903 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_experiment-bioproject.tsv Rule for TSV (output/tsv/sra_experiment-bioproject.tsv) ------------------------------ Investigating output/tsv/sra_experiment-bioproject.tsv @@ -4574,19 +4332,15 @@ task needed: true timestamp: 2024-12-16 17:13:23 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:13:23 +0900) -latest-prerequisite time: 2024-12-16 17:13:23 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_experiment-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_experiment-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_experiment-biosample.tsv is newer than config/sra_experiment-biosample/config.yaml # File output/tsv/sra_experiment-biosample.tsv has no timestamp file -# File output/tsv/sra_experiment-biosample.tsv is created 9.781367928756227 days ago (will be updated when >5 days) -## Update config/sra_experiment-biosample/config.yaml => output/tsv/sra_experiment-biosample.tsv -< 2024-12-16T17:13:23 sra_experiment-biosample -togoid-config config/sra_experiment-biosample update -# Success: output/tsv/sra_experiment-biosample.tsv is updated -> 2024-12-16T17:16:58 sra_experiment-biosample +# File output/tsv/sra_experiment-biosample.tsv is created 4.18042911919206 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_experiment-biosample.tsv Rule for TSV (output/tsv/sra_experiment-biosample.tsv) ------------------------------ Investigating output/tsv/sra_experiment-biosample.tsv @@ -4595,19 +4349,15 @@ task needed: true timestamp: 2024-12-16 17:16:58 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:16:58 +0900) -latest-prerequisite time: 2024-12-16 17:16:58 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_experiment-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_experiment-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_experiment-sra_project.tsv is newer than config/sra_experiment-sra_project/config.yaml # File output/tsv/sra_experiment-sra_project.tsv has no timestamp file -# File output/tsv/sra_experiment-sra_project.tsv is created 9.781753889444143 days ago (will be updated when >5 days) -## Update config/sra_experiment-sra_project/config.yaml => output/tsv/sra_experiment-sra_project.tsv -< 2024-12-16T17:16:58 sra_experiment-sra_project -togoid-config config/sra_experiment-sra_project update -# Success: output/tsv/sra_experiment-sra_project.tsv is updated -> 2024-12-16T17:20:02 sra_experiment-sra_project +# File output/tsv/sra_experiment-sra_project.tsv is created 4.178295914788715 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_experiment-sra_project.tsv Rule for TSV (output/tsv/sra_experiment-sra_project.tsv) ------------------------------ Investigating output/tsv/sra_experiment-sra_project.tsv @@ -4616,19 +4366,15 @@ task needed: true timestamp: 2024-12-16 17:20:02 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:20:02 +0900) -latest-prerequisite time: 2024-12-16 17:20:02 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_experiment-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_experiment-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_experiment-sra_sample.tsv is newer than config/sra_experiment-sra_sample/config.yaml # File output/tsv/sra_experiment-sra_sample.tsv has no timestamp file -# File output/tsv/sra_experiment-sra_sample.tsv is created 9.781835751805717 days ago (will be updated when >5 days) -## Update config/sra_experiment-sra_sample/config.yaml => output/tsv/sra_experiment-sra_sample.tsv -< 2024-12-16T17:20:02 sra_experiment-sra_sample -togoid-config config/sra_experiment-sra_sample update -# Success: output/tsv/sra_experiment-sra_sample.tsv is updated -> 2024-12-16T17:23:00 sra_experiment-sra_sample +# File output/tsv/sra_experiment-sra_sample.tsv is created 4.176239166060394 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_experiment-sra_sample.tsv Rule for TSV (output/tsv/sra_experiment-sra_sample.tsv) ------------------------------ Investigating output/tsv/sra_experiment-sra_sample.tsv @@ -4637,19 +4383,15 @@ task needed: true timestamp: 2024-12-16 17:23:00 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:23:00 +0900) -latest-prerequisite time: 2024-12-16 17:23:00 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_project-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_project-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_project-bioproject.tsv is newer than config/sra_project-bioproject/config.yaml # File output/tsv/sra_project-bioproject.tsv has no timestamp file -# File output/tsv/sra_project-bioproject.tsv is created 9.783072840976608 days ago (will be updated when >5 days) -## Update config/sra_project-bioproject/config.yaml => output/tsv/sra_project-bioproject.tsv -< 2024-12-16T17:23:00 sra_project-bioproject -togoid-config config/sra_project-bioproject update -# Success: output/tsv/sra_project-bioproject.tsv is updated -> 2024-12-16T17:24:09 sra_project-bioproject +# File output/tsv/sra_project-bioproject.tsv is created 4.175438251511285 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_project-bioproject.tsv Rule for TSV (output/tsv/sra_project-bioproject.tsv) ------------------------------ Investigating output/tsv/sra_project-bioproject.tsv @@ -4658,19 +4400,15 @@ task needed: true timestamp: 2024-12-16 17:24:09 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:24:09 +0900) -latest-prerequisite time: 2024-12-16 17:24:09 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_run-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_run-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_run-bioproject.tsv is newer than config/sra_run-bioproject/config.yaml # File output/tsv/sra_run-bioproject.tsv has no timestamp file -# File output/tsv/sra_run-bioproject.tsv is created 9.781023533084294 days ago (will be updated when >5 days) -## Update config/sra_run-bioproject/config.yaml => output/tsv/sra_run-bioproject.tsv -< 2024-12-16T17:24:09 sra_run-bioproject -togoid-config config/sra_run-bioproject update -# Success: output/tsv/sra_run-bioproject.tsv is updated -> 2024-12-16T17:28:18 sra_run-bioproject +# File output/tsv/sra_run-bioproject.tsv is created 4.17256220630684 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_run-bioproject.tsv Rule for TSV (output/tsv/sra_run-bioproject.tsv) ------------------------------ Investigating output/tsv/sra_run-bioproject.tsv @@ -4679,19 +4417,15 @@ task needed: true timestamp: 2024-12-16 17:28:18 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:28:18 +0900) -latest-prerequisite time: 2024-12-16 17:28:18 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_run-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_run-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_run-biosample.tsv is newer than config/sra_run-biosample/config.yaml # File output/tsv/sra_run-biosample.tsv has no timestamp file -# File output/tsv/sra_run-biosample.tsv is created 9.781082013338622 days ago (will be updated when >5 days) -## Update config/sra_run-biosample/config.yaml => output/tsv/sra_run-biosample.tsv -< 2024-12-16T17:28:18 sra_run-biosample -togoid-config config/sra_run-biosample update -# Success: output/tsv/sra_run-biosample.tsv is updated -> 2024-12-16T17:32:19 sra_run-biosample +# File output/tsv/sra_run-biosample.tsv is created 4.16977154347434 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_run-biosample.tsv Rule for TSV (output/tsv/sra_run-biosample.tsv) ------------------------------ Investigating output/tsv/sra_run-biosample.tsv @@ -4700,19 +4434,15 @@ task needed: true timestamp: 2024-12-16 17:32:19 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:32:19 +0900) -latest-prerequisite time: 2024-12-16 17:32:19 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_run-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_run-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_run-sra_experiment.tsv is newer than config/sra_run-sra_experiment/config.yaml # File output/tsv/sra_run-sra_experiment.tsv has no timestamp file -# File output/tsv/sra_run-sra_experiment.tsv is created 9.78172474855309 days ago (will be updated when >5 days) -## Update config/sra_run-sra_experiment/config.yaml => output/tsv/sra_run-sra_experiment.tsv -< 2024-12-16T17:32:19 sra_run-sra_experiment -togoid-config config/sra_run-sra_experiment update -# Success: output/tsv/sra_run-sra_experiment.tsv is updated -> 2024-12-16T17:35:30 sra_run-sra_experiment +# File output/tsv/sra_run-sra_experiment.tsv is created 4.167564033167882 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_run-sra_experiment.tsv Rule for TSV (output/tsv/sra_run-sra_experiment.tsv) ------------------------------ Investigating output/tsv/sra_run-sra_experiment.tsv @@ -4721,19 +4451,15 @@ task needed: true timestamp: 2024-12-16 17:35:30 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:35:30 +0900) -latest-prerequisite time: 2024-12-16 17:35:30 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_run-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_run-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_run-sra_project.tsv is newer than config/sra_run-sra_project/config.yaml # File output/tsv/sra_run-sra_project.tsv has no timestamp file -# File output/tsv/sra_run-sra_project.tsv is created 9.781605915581794 days ago (will be updated when >5 days) -## Update config/sra_run-sra_project/config.yaml => output/tsv/sra_run-sra_project.tsv -< 2024-12-16T17:35:30 sra_run-sra_project -togoid-config config/sra_run-sra_project update -# Success: output/tsv/sra_run-sra_project.tsv is updated -> 2024-12-16T17:38:52 sra_run-sra_project +# File output/tsv/sra_run-sra_project.tsv is created 4.165223166970035 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_run-sra_project.tsv Rule for TSV (output/tsv/sra_run-sra_project.tsv) ------------------------------ Investigating output/tsv/sra_run-sra_project.tsv @@ -4742,19 +4468,15 @@ task needed: true timestamp: 2024-12-16 17:38:52 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:38:52 +0900) -latest-prerequisite time: 2024-12-16 17:38:52 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_run-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_run-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_run-sra_sample.tsv is newer than config/sra_run-sra_sample/config.yaml # File output/tsv/sra_run-sra_sample.tsv has no timestamp file -# File output/tsv/sra_run-sra_sample.tsv is created 9.781702602495614 days ago (will be updated when >5 days) -## Update config/sra_run-sra_sample/config.yaml => output/tsv/sra_run-sra_sample.tsv -< 2024-12-16T17:38:52 sra_run-sra_sample -togoid-config config/sra_run-sra_sample update -# Success: output/tsv/sra_run-sra_sample.tsv is updated -> 2024-12-16T17:42:11 sra_run-sra_sample +# File output/tsv/sra_run-sra_sample.tsv is created 4.162925367183287 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_run-sra_sample.tsv Rule for TSV (output/tsv/sra_run-sra_sample.tsv) ------------------------------ Investigating output/tsv/sra_run-sra_sample.tsv @@ -4763,19 +4485,15 @@ task needed: true timestamp: 2024-12-16 17:42:10 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:42:11 +0900) -latest-prerequisite time: 2024-12-16 17:42:11 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ -### Update TSV for sra_sample-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for sra_sample-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/sra_sample-biosample.tsv is newer than config/sra_sample-biosample/config.yaml # File output/tsv/sra_sample-biosample.tsv has no timestamp file -# File output/tsv/sra_sample-biosample.tsv is created 9.78177955850214 days ago (will be updated when >5 days) -## Update config/sra_sample-biosample/config.yaml => output/tsv/sra_sample-biosample.tsv -< 2024-12-16T17:42:11 sra_sample-biosample -togoid-config config/sra_sample-biosample update -# Success: output/tsv/sra_sample-biosample.tsv is updated -> 2024-12-16T17:45:26 sra_sample-biosample +# File output/tsv/sra_sample-biosample.tsv is created 4.160662185727998 days ago (will be updated when >5 days) +# => Preserving output/tsv/sra_sample-biosample.tsv Rule for TSV (output/tsv/sra_sample-biosample.tsv) ------------------------------ Investigating output/tsv/sra_sample-biosample.tsv @@ -4784,278 +4502,242 @@ task needed: true timestamp: 2024-12-16 17:45:26 +0900 pre-requisites: --output/tsv/ () ---prepare:sra (2024-12-16 17:45:26 +0900) -latest-prerequisite time: 2024-12-16 17:45:26 +0900 +--prepare:sra (2024-12-20 21:36:47 +0900) +latest-prerequisite time: 2024-12-20 21:36:47 +0900 ................................ ### Update TSV for swisslipids-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/swisslipids-chebi.tsv is newer than config/swisslipids-chebi/config.yaml # File output/tsv/swisslipids-chebi.tsv is older than input/swisslipids/download.lock ## Update config/swisslipids-chebi/config.yaml => output/tsv/swisslipids-chebi.tsv -< 2024-12-16T17:45:26 swisslipids-chebi +< 2024-12-20T21:36:47 swisslipids-chebi togoid-config config/swisslipids-chebi update # Success: output/tsv/swisslipids-chebi.tsv is updated -> 2024-12-16T17:45:40 swisslipids-chebi +> 2024-12-20T21:37:03 swisslipids-chebi Rule for TSV (output/tsv/swisslipids-chebi.tsv) ------------------------------ Investigating output/tsv/swisslipids-chebi.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 17:45:40 +0900 +timestamp: 2024-12-20 21:37:03 +0900 pre-requisites: --output/tsv/ () ---prepare:swisslipids (2024-12-16 17:45:40 +0900) -latest-prerequisite time: 2024-12-16 17:45:40 +0900 +--prepare:swisslipids (2024-12-20 21:37:03 +0900) +latest-prerequisite time: 2024-12-20 21:37:03 +0900 ................................ ### Update TSV for swisslipids-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/swisslipids-hmdb.tsv is newer than config/swisslipids-hmdb/config.yaml # File output/tsv/swisslipids-hmdb.tsv is older than input/swisslipids/download.lock ## Update config/swisslipids-hmdb/config.yaml => output/tsv/swisslipids-hmdb.tsv -< 2024-12-16T17:45:40 swisslipids-hmdb +< 2024-12-20T21:37:03 swisslipids-hmdb togoid-config config/swisslipids-hmdb update # Success: output/tsv/swisslipids-hmdb.tsv is updated -> 2024-12-16T17:45:53 swisslipids-hmdb +> 2024-12-20T21:37:17 swisslipids-hmdb Rule for TSV (output/tsv/swisslipids-hmdb.tsv) ------------------------------ Investigating output/tsv/swisslipids-hmdb.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 17:45:53 +0900 +timestamp: 2024-12-20 21:37:17 +0900 pre-requisites: --output/tsv/ () ---prepare:swisslipids (2024-12-16 17:45:53 +0900) -latest-prerequisite time: 2024-12-16 17:45:53 +0900 +--prepare:swisslipids (2024-12-20 21:37:17 +0900) +latest-prerequisite time: 2024-12-20 21:37:17 +0900 ................................ ### Update TSV for swisslipids-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/swisslipids-inchi_key.tsv is newer than config/swisslipids-inchi_key/config.yaml # File output/tsv/swisslipids-inchi_key.tsv is older than input/swisslipids/download.lock ## Update config/swisslipids-inchi_key/config.yaml => output/tsv/swisslipids-inchi_key.tsv -< 2024-12-16T17:45:53 swisslipids-inchi_key +< 2024-12-20T21:37:17 swisslipids-inchi_key togoid-config config/swisslipids-inchi_key update # Success: output/tsv/swisslipids-inchi_key.tsv is updated -> 2024-12-16T17:46:06 swisslipids-inchi_key +> 2024-12-20T21:37:29 swisslipids-inchi_key Rule for TSV (output/tsv/swisslipids-inchi_key.tsv) ------------------------------ Investigating output/tsv/swisslipids-inchi_key.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 17:46:06 +0900 +timestamp: 2024-12-20 21:37:29 +0900 pre-requisites: --output/tsv/ () ---prepare:swisslipids (2024-12-16 17:46:06 +0900) -latest-prerequisite time: 2024-12-16 17:46:06 +0900 +--prepare:swisslipids (2024-12-20 21:37:29 +0900) +latest-prerequisite time: 2024-12-20 21:37:29 +0900 ................................ ### Update TSV for taxonomy-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/taxonomy-pubmed.tsv is newer than config/taxonomy-pubmed/config.yaml # File output/tsv/taxonomy-pubmed.tsv is older than input/taxonomy/download.lock ## Update config/taxonomy-pubmed/config.yaml => output/tsv/taxonomy-pubmed.tsv -< 2024-12-16T17:46:06 taxonomy-pubmed +< 2024-12-20T21:37:29 taxonomy-pubmed togoid-config config/taxonomy-pubmed update awk: cmd. line:1: warning: escape sequence `\|' treated as plain `|' # Success: output/tsv/taxonomy-pubmed.tsv is updated -> 2024-12-16T17:46:06 taxonomy-pubmed +> 2024-12-20T21:37:30 taxonomy-pubmed Rule for TSV (output/tsv/taxonomy-pubmed.tsv) ------------------------------ Investigating output/tsv/taxonomy-pubmed.tsv class: Rake::FileTask task needed: true -timestamp: 2024-12-16 17:46:06 +0900 +timestamp: 2024-12-20 21:37:30 +0900 pre-requisites: --output/tsv/ () ---prepare:taxonomy (2024-12-16 17:46:06 +0900) -latest-prerequisite time: 2024-12-16 17:46:06 +0900 +--prepare:taxonomy (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ -### Update TSV for togovar-clinvar if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-clinvar if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-clinvar.tsv is newer than config/togovar-clinvar/config.yaml # File output/tsv/togovar-clinvar.tsv has no timestamp file -# File output/tsv/togovar-clinvar.tsv is created 9.783154605086157 days ago (will be updated when >5 days) -## Update config/togovar-clinvar/config.yaml => output/tsv/togovar-clinvar.tsv -< 2024-12-16T17:46:06 togovar-clinvar -togoid-config config/togovar-clinvar update -# Success: output/tsv/togovar-clinvar.tsv is updated -> 2024-12-16T17:47:06 togovar-clinvar +# File output/tsv/togovar-clinvar.tsv is created 4.159996733809005 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-clinvar.tsv Rule for TSV (output/tsv/togovar-clinvar.tsv) ------------------------------ Investigating output/tsv/togovar-clinvar.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:47:06 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-dbsnp.tsv is newer than config/togovar-dbsnp/config.yaml # File output/tsv/togovar-dbsnp.tsv has no timestamp file -# File output/tsv/togovar-dbsnp.tsv is created 9.783446234648691 days ago (will be updated when >5 days) -## Update config/togovar-dbsnp/config.yaml => output/tsv/togovar-dbsnp.tsv -< 2024-12-16T17:47:06 togovar-dbsnp -togoid-config config/togovar-dbsnp update -# Success: output/tsv/togovar-dbsnp.tsv is updated -> 2024-12-16T17:47:41 togovar-dbsnp +# File output/tsv/togovar-dbsnp.tsv is created 4.159588252859282 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-dbsnp.tsv Rule for TSV (output/tsv/togovar-dbsnp.tsv) ------------------------------ Investigating output/tsv/togovar-dbsnp.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:47:41 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-ensembl_gene.tsv is newer than config/togovar-ensembl_gene/config.yaml # File output/tsv/togovar-ensembl_gene.tsv has no timestamp file -# File output/tsv/togovar-ensembl_gene.tsv is created 9.783399154122176 days ago (will be updated when >5 days) -## Update config/togovar-ensembl_gene/config.yaml => output/tsv/togovar-ensembl_gene.tsv -< 2024-12-16T17:47:41 togovar-ensembl_gene -togoid-config config/togovar-ensembl_gene update -# Success: output/tsv/togovar-ensembl_gene.tsv is updated -> 2024-12-16T17:48:22 togovar-ensembl_gene +# File output/tsv/togovar-ensembl_gene.tsv is created 4.159121287377639 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-ensembl_gene.tsv Rule for TSV (output/tsv/togovar-ensembl_gene.tsv) ------------------------------ Investigating output/tsv/togovar-ensembl_gene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:48:22 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-ensembl_transcript.tsv is newer than config/togovar-ensembl_transcript/config.yaml # File output/tsv/togovar-ensembl_transcript.tsv has no timestamp file -# File output/tsv/togovar-ensembl_transcript.tsv is created 16.548597532308285 days ago (will be updated when >5 days) -## Update config/togovar-ensembl_transcript/config.yaml => output/tsv/togovar-ensembl_transcript.tsv -< 2024-12-16T17:48:22 togovar-ensembl_transcript -togoid-config config/togovar-ensembl_transcript update -# Success: output/tsv/togovar-ensembl_transcript.tsv is updated -> 2024-12-16T17:50:47 togovar-ensembl_transcript +# File output/tsv/togovar-ensembl_transcript.tsv is created 4.157441465936227 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-ensembl_transcript.tsv Rule for TSV (output/tsv/togovar-ensembl_transcript.tsv) ------------------------------ Investigating output/tsv/togovar-ensembl_transcript.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:50:47 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-hgnc.tsv is newer than config/togovar-hgnc/config.yaml # File output/tsv/togovar-hgnc.tsv has no timestamp file -# File output/tsv/togovar-hgnc.tsv is created 9.78526268543397 days ago (will be updated when >5 days) -## Update config/togovar-hgnc/config.yaml => output/tsv/togovar-hgnc.tsv -< 2024-12-16T17:50:47 togovar-hgnc -togoid-config config/togovar-hgnc update -# Success: output/tsv/togovar-hgnc.tsv is updated -> 2024-12-16T17:51:10 togovar-hgnc +# File output/tsv/togovar-hgnc.tsv is created 4.157169432155845 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-hgnc.tsv Rule for TSV (output/tsv/togovar-hgnc.tsv) ------------------------------ Investigating output/tsv/togovar-hgnc.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:51:10 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-ncbigene.tsv is newer than config/togovar-ncbigene/config.yaml # File output/tsv/togovar-ncbigene.tsv has no timestamp file -# File output/tsv/togovar-ncbigene.tsv is created 16.54998045762058 days ago (will be updated when >5 days) -## Update config/togovar-ncbigene/config.yaml => output/tsv/togovar-ncbigene.tsv -< 2024-12-16T17:51:10 togovar-ncbigene -togoid-config config/togovar-ncbigene update -# Success: output/tsv/togovar-ncbigene.tsv is updated -> 2024-12-16T17:51:33 togovar-ncbigene +# File output/tsv/togovar-ncbigene.tsv is created 4.156903744906875 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-ncbigene.tsv Rule for TSV (output/tsv/togovar-ncbigene.tsv) ------------------------------ Investigating output/tsv/togovar-ncbigene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:51:33 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-pubmed.tsv is newer than config/togovar-pubmed/config.yaml # File output/tsv/togovar-pubmed.tsv has no timestamp file -# File output/tsv/togovar-pubmed.tsv is created 16.550236571725172 days ago (will be updated when >5 days) -## Update config/togovar-pubmed/config.yaml => output/tsv/togovar-pubmed.tsv -< 2024-12-16T17:51:33 togovar-pubmed -togoid-config config/togovar-pubmed update -# Success: output/tsv/togovar-pubmed.tsv is updated -> 2024-12-16T17:51:34 togovar-pubmed +# File output/tsv/togovar-pubmed.tsv is created 4.156894803228657 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-pubmed.tsv Rule for TSV (output/tsv/togovar-pubmed.tsv) ------------------------------ Investigating output/tsv/togovar-pubmed.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:51:34 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for togovar-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for togovar-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/togovar-refseq_rna.tsv is newer than config/togovar-refseq_rna/config.yaml # File output/tsv/togovar-refseq_rna.tsv has no timestamp file -# File output/tsv/togovar-refseq_rna.tsv is created 16.54928088685285 days ago (will be updated when >5 days) -## Update config/togovar-refseq_rna/config.yaml => output/tsv/togovar-refseq_rna.tsv -< 2024-12-16T17:51:34 togovar-refseq_rna -togoid-config config/togovar-refseq_rna update -# Success: output/tsv/togovar-refseq_rna.tsv is updated -> 2024-12-16T17:53:04 togovar-refseq_rna +# File output/tsv/togovar-refseq_rna.tsv is created 4.155858088327858 days ago (will be updated when >5 days) +# => Preserving output/tsv/togovar-refseq_rna.tsv Rule for TSV (output/tsv/togovar-refseq_rna.tsv) ------------------------------ Investigating output/tsv/togovar-refseq_rna.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:04 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for uberon-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for uberon-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/uberon-ncit_tissue.tsv is newer than config/uberon-ncit_tissue/config.yaml # File output/tsv/uberon-ncit_tissue.tsv has no timestamp file -# File output/tsv/uberon-ncit_tissue.tsv is created 16.550294377350234 days ago (will be updated when >5 days) -## Update config/uberon-ncit_tissue/config.yaml => output/tsv/uberon-ncit_tissue.tsv -< 2024-12-16T17:53:04 uberon-ncit_tissue -togoid-config config/uberon-ncit_tissue update -# Success: output/tsv/uberon-ncit_tissue.tsv is updated -> 2024-12-16T17:53:05 uberon-ncit_tissue +# File output/tsv/uberon-ncit_tissue.tsv is created 4.155835512230787 days ago (will be updated when >5 days) +# => Preserving output/tsv/uberon-ncit_tissue.tsv Rule for TSV (output/tsv/uberon-ncit_tissue.tsv) ------------------------------ Investigating output/tsv/uberon-ncit_tissue.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:05 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for uniprot-chembl_target if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5070,8 +4752,8 @@ task needed: true timestamp: 2024-11-30 05:19:45 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5086,8 +4768,8 @@ task needed: true timestamp: 2024-11-30 05:20:10 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5102,8 +4784,8 @@ task needed: true timestamp: 2024-11-30 05:55:03 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5118,8 +4800,8 @@ task needed: true timestamp: 2024-11-30 06:42:45 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-ensembl_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5134,8 +4816,8 @@ task needed: true timestamp: 2024-11-30 07:29:45 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5150,8 +4832,8 @@ task needed: true timestamp: 2024-11-30 08:16:54 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5166,8 +4848,8 @@ task needed: true timestamp: 2024-11-30 08:36:07 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5182,8 +4864,8 @@ task needed: true timestamp: 2024-11-30 09:14:30 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5198,8 +4880,8 @@ task needed: true timestamp: 2024-11-30 10:00:39 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-intact if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5214,8 +4896,8 @@ task needed: true timestamp: 2024-11-30 10:02:02 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5230,8 +4912,8 @@ task needed: true timestamp: 2024-11-30 10:41:09 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-oma_group if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5246,8 +4928,8 @@ task needed: true timestamp: 2024-11-30 11:20:53 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5262,8 +4944,8 @@ task needed: true timestamp: 2024-11-30 11:21:01 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5278,8 +4960,8 @@ task needed: true timestamp: 2024-11-30 11:21:04 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5294,8 +4976,8 @@ task needed: true timestamp: 2024-11-30 12:07:53 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5310,8 +4992,8 @@ task needed: true timestamp: 2024-11-30 12:47:53 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5326,8 +5008,8 @@ task needed: true timestamp: 2024-11-30 13:34:50 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5342,8 +5024,8 @@ task needed: true timestamp: 2024-11-30 14:15:09 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5358,8 +5040,8 @@ task needed: true timestamp: 2024-11-30 14:50:01 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ ### Update TSV for uniprot-uniprot_mnemonic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false @@ -5374,19 +5056,15 @@ task needed: true timestamp: 2024-11-30 15:46:15 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ -### Update TSV for uniprot_proteome-assembly_insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for uniprot_proteome-assembly_insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/uniprot_proteome-assembly_insdc.tsv is newer than config/uniprot_proteome-assembly_insdc/config.yaml # File output/tsv/uniprot_proteome-assembly_insdc.tsv has no timestamp file -# File output/tsv/uniprot_proteome-assembly_insdc.tsv is created 9.785312810719804 days ago (will be updated when >5 days) -## Update config/uniprot_proteome-assembly_insdc/config.yaml => output/tsv/uniprot_proteome-assembly_insdc.tsv -< 2024-12-16T17:53:06 uniprot_proteome-assembly_insdc -togoid-config config/uniprot_proteome-assembly_insdc update -# Success: output/tsv/uniprot_proteome-assembly_insdc.tsv is updated -> 2024-12-16T17:53:06 uniprot_proteome-assembly_insdc +# File output/tsv/uniprot_proteome-assembly_insdc.tsv is created 4.155828082572547 days ago (will be updated when >5 days) +# => Preserving output/tsv/uniprot_proteome-assembly_insdc.tsv Rule for TSV (output/tsv/uniprot_proteome-assembly_insdc.tsv) ------------------------------ Investigating output/tsv/uniprot_proteome-assembly_insdc.tsv @@ -5395,19 +5073,15 @@ task needed: true timestamp: 2024-12-16 17:53:06 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:06 +0900) -latest-prerequisite time: 2024-12-16 17:53:06 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ -### Update TSV for uniprot_proteome-assembly_refseq if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for uniprot_proteome-assembly_refseq if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/uniprot_proteome-assembly_refseq.tsv is newer than config/uniprot_proteome-assembly_refseq/config.yaml # File output/tsv/uniprot_proteome-assembly_refseq.tsv has no timestamp file -# File output/tsv/uniprot_proteome-assembly_refseq.tsv is created 9.785315376536806 days ago (will be updated when >5 days) -## Update config/uniprot_proteome-assembly_refseq/config.yaml => output/tsv/uniprot_proteome-assembly_refseq.tsv -< 2024-12-16T17:53:06 uniprot_proteome-assembly_refseq -togoid-config config/uniprot_proteome-assembly_refseq update -# Success: output/tsv/uniprot_proteome-assembly_refseq.tsv is updated -> 2024-12-16T17:53:07 uniprot_proteome-assembly_refseq +# File output/tsv/uniprot_proteome-assembly_refseq.tsv is created 4.155821270672164 days ago (will be updated when >5 days) +# => Preserving output/tsv/uniprot_proteome-assembly_refseq.tsv Rule for TSV (output/tsv/uniprot_proteome-assembly_refseq.tsv) ------------------------------ Investigating output/tsv/uniprot_proteome-assembly_refseq.tsv @@ -5416,19 +5090,15 @@ task needed: true timestamp: 2024-12-16 17:53:07 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:07 +0900) -latest-prerequisite time: 2024-12-16 17:53:07 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ -### Update TSV for uniprot_proteome-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for uniprot_proteome-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/uniprot_proteome-taxonomy.tsv is newer than config/uniprot_proteome-taxonomy/config.yaml # File output/tsv/uniprot_proteome-taxonomy.tsv has no timestamp file -# File output/tsv/uniprot_proteome-taxonomy.tsv is created 9.78531575523875 days ago (will be updated when >5 days) -## Update config/uniprot_proteome-taxonomy/config.yaml => output/tsv/uniprot_proteome-taxonomy.tsv -< 2024-12-16T17:53:07 uniprot_proteome-taxonomy -togoid-config config/uniprot_proteome-taxonomy update -# Success: output/tsv/uniprot_proteome-taxonomy.tsv is updated -> 2024-12-16T17:53:07 uniprot_proteome-taxonomy +# File output/tsv/uniprot_proteome-taxonomy.tsv is created 4.155814701597963 days ago (will be updated when >5 days) +# => Preserving output/tsv/uniprot_proteome-taxonomy.tsv Rule for TSV (output/tsv/uniprot_proteome-taxonomy.tsv) ------------------------------ Investigating output/tsv/uniprot_proteome-taxonomy.tsv @@ -5437,125 +5107,105 @@ task needed: true timestamp: 2024-12-16 17:53:07 +0900 pre-requisites: --output/tsv/ () ---prepare:uniprot (2024-12-16 17:53:07 +0900) -latest-prerequisite time: 2024-12-16 17:53:07 +0900 +--prepare:uniprot (2024-12-20 21:37:30 +0900) +latest-prerequisite time: 2024-12-20 21:37:30 +0900 ................................ -### Update TSV for wikipathways-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for wikipathways-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/wikipathways-chebi.tsv is newer than config/wikipathways-chebi/config.yaml # File output/tsv/wikipathways-chebi.tsv has no timestamp file -# File output/tsv/wikipathways-chebi.tsv is created 9.785274941143113 days ago (will be updated when >5 days) -## Update config/wikipathways-chebi/config.yaml => output/tsv/wikipathways-chebi.tsv -< 2024-12-16T17:53:07 wikipathways-chebi -togoid-config config/wikipathways-chebi update -# Success: output/tsv/wikipathways-chebi.tsv is updated -> 2024-12-16T17:53:12 wikipathways-chebi +# File output/tsv/wikipathways-chebi.tsv is created 4.155766257310683 days ago (will be updated when >5 days) +# => Preserving output/tsv/wikipathways-chebi.tsv Rule for TSV (output/tsv/wikipathways-chebi.tsv) ------------------------------ Investigating output/tsv/wikipathways-chebi.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:12 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for wikipathways-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for wikipathways-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/wikipathways-doid.tsv is newer than config/wikipathways-doid/config.yaml # File output/tsv/wikipathways-doid.tsv has no timestamp file -# File output/tsv/wikipathways-doid.tsv is created 9.785302295269455 days ago (will be updated when >5 days) -## Update config/wikipathways-doid/config.yaml => output/tsv/wikipathways-doid.tsv -< 2024-12-16T17:53:12 wikipathways-doid -togoid-config config/wikipathways-doid update -# Success: output/tsv/wikipathways-doid.tsv is updated -> 2024-12-16T17:53:13 wikipathways-doid +# File output/tsv/wikipathways-doid.tsv is created 4.155745186248298 days ago (will be updated when >5 days) +# => Preserving output/tsv/wikipathways-doid.tsv Rule for TSV (output/tsv/wikipathways-doid.tsv) ------------------------------ Investigating output/tsv/wikipathways-doid.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:13 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for wikipathways-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for wikipathways-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/wikipathways-hmdb.tsv is newer than config/wikipathways-hmdb/config.yaml # File output/tsv/wikipathways-hmdb.tsv has no timestamp file -# File output/tsv/wikipathways-hmdb.tsv is created 9.785299659231239 days ago (will be updated when >5 days) -## Update config/wikipathways-hmdb/config.yaml => output/tsv/wikipathways-hmdb.tsv -< 2024-12-16T17:53:13 wikipathways-hmdb -togoid-config config/wikipathways-hmdb update -# Success: output/tsv/wikipathways-hmdb.tsv is updated -> 2024-12-16T17:53:16 wikipathways-hmdb +# File output/tsv/wikipathways-hmdb.tsv is created 4.155719241967477 days ago (will be updated when >5 days) +# => Preserving output/tsv/wikipathways-hmdb.tsv Rule for TSV (output/tsv/wikipathways-hmdb.tsv) ------------------------------ Investigating output/tsv/wikipathways-hmdb.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:16 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for wikipathways-lipidmaps if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for wikipathways-lipidmaps if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/wikipathways-lipidmaps.tsv is newer than config/wikipathways-lipidmaps/config.yaml # File output/tsv/wikipathways-lipidmaps.tsv has no timestamp file -# File output/tsv/wikipathways-lipidmaps.tsv is created 9.785304262861807 days ago (will be updated when >5 days) -## Update config/wikipathways-lipidmaps/config.yaml => output/tsv/wikipathways-lipidmaps.tsv -< 2024-12-16T17:53:16 wikipathways-lipidmaps -togoid-config config/wikipathways-lipidmaps update -# Success: output/tsv/wikipathways-lipidmaps.tsv is updated -> 2024-12-16T17:53:17 wikipathways-lipidmaps +# File output/tsv/wikipathways-lipidmaps.tsv is created 4.155697559005949 days ago (will be updated when >5 days) +# => Preserving output/tsv/wikipathways-lipidmaps.tsv Rule for TSV (output/tsv/wikipathways-lipidmaps.tsv) ------------------------------ Investigating output/tsv/wikipathways-lipidmaps.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:17 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ -### Update TSV for wikipathways-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true +### Update TSV for wikipathways-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false # File output/tsv/wikipathways-ncbigene.tsv is newer than config/wikipathways-ncbigene/config.yaml # File output/tsv/wikipathways-ncbigene.tsv has no timestamp file -# File output/tsv/wikipathways-ncbigene.tsv is created 9.78516847207868 days ago (will be updated when >5 days) -## Update config/wikipathways-ncbigene/config.yaml => output/tsv/wikipathways-ncbigene.tsv -< 2024-12-16T17:53:17 wikipathways-ncbigene -togoid-config config/wikipathways-ncbigene update -# Success: output/tsv/wikipathways-ncbigene.tsv is updated -> 2024-12-16T17:53:31 wikipathways-ncbigene +# File output/tsv/wikipathways-ncbigene.tsv is created 4.1555360788109255 days ago (will be updated when >5 days) +# => Preserving output/tsv/wikipathways-ncbigene.tsv Rule for TSV (output/tsv/wikipathways-ncbigene.tsv) ------------------------------ Investigating output/tsv/wikipathways-ncbigene.tsv class: Rake::FileTask -task needed: false +task needed: true timestamp: 2024-12-16 17:53:31 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TSV for wikipathways-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true # File output/tsv/wikipathways-uniprot.tsv is newer than config/wikipathways-uniprot/config.yaml # File output/tsv/wikipathways-uniprot.tsv has no timestamp file -# File output/tsv/wikipathways-uniprot.tsv is created 282.7555997254527 days ago (will be updated when >5 days) +# File output/tsv/wikipathways-uniprot.tsv is created 286.91113579283325 days ago (will be updated when >5 days) ## Update config/wikipathways-uniprot/config.yaml => output/tsv/wikipathways-uniprot.tsv -< 2024-12-16T17:53:31 wikipathways-uniprot +< 2024-12-20T21:37:30 wikipathways-uniprot togoid-config config/wikipathways-uniprot update # Error: output/tsv/wikipathways-uniprot.tsv new file size per old 60240 / 470542 = 0.12802257821830995 < 0.5 # Failure: output/tsv/wikipathways-uniprot.tsv is not updated -> 2024-12-16T17:53:36 wikipathways-uniprot +> 2024-12-20T21:37:34 wikipathways-uniprot Rule for TSV (output/tsv/wikipathways-uniprot.tsv) ------------------------------ Investigating output/tsv/wikipathways-uniprot.tsv @@ -5564,98 +5214,95 @@ task needed: true timestamp: 2024-03-08 23:45:28 +0900 pre-requisites: --output/tsv/ () ---input/update.txt (2024-12-16 01:06:15 +0900) -latest-prerequisite time: 2024-12-16 01:06:15 +0900 +--input/update.txt (2024-12-20 20:08:23 +0900) +latest-prerequisite time: 2024-12-20 20:08:23 +0900 ................................ ### Update TTL for affy_probeset-ncbigene if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/affy_probeset-ncbigene.ttl is older than output/tsv/affy_probeset-ncbigene.tsv ## Convert output/tsv/affy_probeset-ncbigene.tsv => output/ttl/relation/affy_probeset-ncbigene.ttl -< 2024-12-16T17:53:36 affy_probeset-ncbigene +< 2024-12-20T21:37:34 affy_probeset-ncbigene togoid-config config/affy_probeset-ncbigene convert -> 2024-12-16T17:53:36 affy_probeset-ncbigene +> 2024-12-20T21:37:35 affy_probeset-ncbigene ### Update TTL for assembly_insdc-bioproject if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/assembly_insdc-bioproject.ttl is older than output/tsv/assembly_insdc-bioproject.tsv ## Convert output/tsv/assembly_insdc-bioproject.tsv => output/ttl/relation/assembly_insdc-bioproject.ttl -< 2024-12-16T17:53:36 assembly_insdc-bioproject +< 2024-12-20T21:37:35 assembly_insdc-bioproject togoid-config config/assembly_insdc-bioproject convert -> 2024-12-16T17:53:56 assembly_insdc-bioproject +> 2024-12-20T21:37:54 assembly_insdc-bioproject ### Update TTL for assembly_insdc-biosample if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/assembly_insdc-biosample.ttl is older than output/tsv/assembly_insdc-biosample.tsv ## Convert output/tsv/assembly_insdc-biosample.tsv => output/ttl/relation/assembly_insdc-biosample.ttl -< 2024-12-16T17:53:56 assembly_insdc-biosample +< 2024-12-20T21:37:54 assembly_insdc-biosample togoid-config config/assembly_insdc-biosample convert -> 2024-12-16T17:54:15 assembly_insdc-biosample +> 2024-12-20T21:38:14 assembly_insdc-biosample ### Update TTL for assembly_insdc-insdc_master if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/assembly_insdc-insdc_master.ttl is older than output/tsv/assembly_insdc-insdc_master.tsv ## Convert output/tsv/assembly_insdc-insdc_master.tsv => output/ttl/relation/assembly_insdc-insdc_master.ttl -< 2024-12-16T17:54:15 assembly_insdc-insdc_master +< 2024-12-20T21:38:14 assembly_insdc-insdc_master togoid-config config/assembly_insdc-insdc_master convert -> 2024-12-16T17:54:34 assembly_insdc-insdc_master +> 2024-12-20T21:38:32 assembly_insdc-insdc_master ### Update TTL for bioproject-biosample if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/bioproject-biosample.ttl is older than output/tsv/bioproject-biosample.tsv ## Convert output/tsv/bioproject-biosample.tsv => output/ttl/relation/bioproject-biosample.ttl -< 2024-12-16T17:54:34 bioproject-biosample +< 2024-12-20T21:38:32 bioproject-biosample togoid-config config/bioproject-biosample convert -> 2024-12-16T17:54:55 bioproject-biosample +> 2024-12-20T21:41:39 bioproject-biosample ### Update TTL for bioproject-geo_series if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/bioproject-geo_series.ttl is older than output/tsv/bioproject-geo_series.tsv ## Convert output/tsv/bioproject-geo_series.tsv => output/ttl/relation/bioproject-geo_series.ttl -< 2024-12-16T17:54:55 bioproject-geo_series +< 2024-12-20T21:41:39 bioproject-geo_series togoid-config config/bioproject-geo_series convert -> 2024-12-16T17:54:57 bioproject-geo_series +> 2024-12-20T21:41:41 bioproject-geo_series ### Update TTL for bioproject-pubmed if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/bioproject-pubmed.ttl is older than output/tsv/bioproject-pubmed.tsv ## Convert output/tsv/bioproject-pubmed.tsv => output/ttl/relation/bioproject-pubmed.ttl -< 2024-12-16T17:54:57 bioproject-pubmed +< 2024-12-20T21:41:41 bioproject-pubmed togoid-config config/bioproject-pubmed convert -> 2024-12-16T17:55:00 bioproject-pubmed +> 2024-12-20T21:41:44 bioproject-pubmed ### Update TTL for bioproject_umbrella-bioproject if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/bioproject_umbrella-bioproject.ttl is older than output/tsv/bioproject_umbrella-bioproject.tsv ## Convert output/tsv/bioproject_umbrella-bioproject.tsv => output/ttl/relation/bioproject_umbrella-bioproject.ttl -< 2024-12-16T17:55:00 bioproject_umbrella-bioproject +< 2024-12-20T21:41:44 bioproject_umbrella-bioproject togoid-config config/bioproject_umbrella-bioproject convert -> 2024-12-16T17:55:01 bioproject_umbrella-bioproject +> 2024-12-20T21:41:45 bioproject_umbrella-bioproject ### Update TTL for biosample-bioproject if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/biosample-bioproject.ttl is older than output/tsv/biosample-bioproject.tsv ## Convert output/tsv/biosample-bioproject.tsv => output/ttl/relation/biosample-bioproject.ttl -< 2024-12-16T17:55:01 biosample-bioproject +< 2024-12-20T21:41:45 biosample-bioproject togoid-config config/biosample-bioproject convert -> 2024-12-16T17:57:56 biosample-bioproject +> 2024-12-20T21:45:01 biosample-bioproject ### Update TTL for biosample-geo_sample if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/biosample-geo_sample.ttl is older than output/tsv/biosample-geo_sample.tsv ## Convert output/tsv/biosample-geo_sample.tsv => output/ttl/relation/biosample-geo_sample.ttl -< 2024-12-16T17:57:56 biosample-geo_sample +< 2024-12-20T21:45:01 biosample-geo_sample togoid-config config/biosample-geo_sample convert -> 2024-12-16T17:59:11 biosample-geo_sample -### Update TTL for cellosaurus-ncit_disease if check_ttl_filesize false or check_ttl_timestamp false -# File output/ttl/relation/cellosaurus-ncit_disease.ttl is newer than output/tsv/cellosaurus-ncit_disease.tsv -# => Preserving output/ttl/relation/cellosaurus-ncit_disease.ttl -### Update TTL for cellosaurus-orphanet_phenotype if check_ttl_filesize false or check_ttl_timestamp false -# File output/ttl/relation/cellosaurus-orphanet_phenotype.ttl is newer than output/tsv/cellosaurus-orphanet_phenotype.tsv -# => Preserving output/ttl/relation/cellosaurus-orphanet_phenotype.ttl -### Update TTL for chebi-glytoucan if check_ttl_filesize false or check_ttl_timestamp true -# File output/ttl/relation/chebi-glytoucan.ttl is older than output/tsv/chebi-glytoucan.tsv -## Convert output/tsv/chebi-glytoucan.tsv => output/ttl/relation/chebi-glytoucan.ttl -< 2024-12-16T17:59:11 chebi-glytoucan -togoid-config config/chebi-glytoucan convert -> 2024-12-16T17:59:12 chebi-glytoucan -### Update TTL for chebi-inchi_key if check_ttl_filesize false or check_ttl_timestamp true -# File output/ttl/relation/chebi-inchi_key.ttl is older than output/tsv/chebi-inchi_key.tsv -## Convert output/tsv/chebi-inchi_key.tsv => output/ttl/relation/chebi-inchi_key.ttl -< 2024-12-16T17:59:12 chebi-inchi_key -togoid-config config/chebi-inchi_key convert -> 2024-12-16T17:59:13 chebi-inchi_key -### Update TTL for chembl_compound-chebi if check_ttl_filesize false or check_ttl_timestamp true -# File output/ttl/relation/chembl_compound-chebi.ttl is older than output/tsv/chembl_compound-chebi.tsv -## Convert output/tsv/chembl_compound-chebi.tsv => output/ttl/relation/chembl_compound-chebi.ttl -< 2024-12-16T17:59:13 chembl_compound-chebi -togoid-config config/chembl_compound-chebi convert -> 2024-12-16T17:59:14 chembl_compound-chebi +> 2024-12-20T21:46:20 biosample-geo_sample +### Update TTL for cellosaurus-ncit_disease if check_ttl_filesize false or check_ttl_timestamp true +# File output/ttl/relation/cellosaurus-ncit_disease.ttl is older than output/tsv/cellosaurus-ncit_disease.tsv +## Convert output/tsv/cellosaurus-ncit_disease.tsv => output/ttl/relation/cellosaurus-ncit_disease.ttl +< 2024-12-20T21:46:20 cellosaurus-ncit_disease +togoid-config config/cellosaurus-ncit_disease convert +> 2024-12-20T21:46:21 cellosaurus-ncit_disease +### Update TTL for cellosaurus-orphanet_phenotype if check_ttl_filesize false or check_ttl_timestamp true +# File output/ttl/relation/cellosaurus-orphanet_phenotype.ttl is older than output/tsv/cellosaurus-orphanet_phenotype.tsv +## Convert output/tsv/cellosaurus-orphanet_phenotype.tsv => output/ttl/relation/cellosaurus-orphanet_phenotype.ttl +< 2024-12-20T21:46:21 cellosaurus-orphanet_phenotype +togoid-config config/cellosaurus-orphanet_phenotype convert +> 2024-12-20T21:46:21 cellosaurus-orphanet_phenotype +### Update TTL for chebi-glytoucan if check_ttl_filesize false or check_ttl_timestamp false +# File output/ttl/relation/chebi-glytoucan.ttl is newer than output/tsv/chebi-glytoucan.tsv +# => Preserving output/ttl/relation/chebi-glytoucan.ttl +### Update TTL for chebi-inchi_key if check_ttl_filesize false or check_ttl_timestamp false +# File output/ttl/relation/chebi-inchi_key.ttl is newer than output/tsv/chebi-inchi_key.tsv +# => Preserving output/ttl/relation/chebi-inchi_key.ttl +### Update TTL for chembl_compound-chebi if check_ttl_filesize false or check_ttl_timestamp false +# File output/ttl/relation/chembl_compound-chebi.ttl is newer than output/tsv/chembl_compound-chebi.tsv +# => Preserving output/ttl/relation/chembl_compound-chebi.ttl ### Update TTL for chembl_compound-chembl_target if check_ttl_filesize false or check_ttl_timestamp true # File output/ttl/relation/chembl_compound-chembl_target.ttl is older than output/tsv/chembl_compound-chembl_target.tsv ## Convert output/tsv/chembl_compound-chembl_target.tsv => output/ttl/relation/chembl_compound-chembl_target.ttl -< 2024-12-16T17:59:14 chembl_compound-chembl_target +< 2024-12-20T21:46:21 chembl_compound-chembl_target togoid-config config/chembl_compound-chembl_target convert /data/togoid/git/togoid-config/lib/togoid-config.rb:237:in `initialize': Permission denied @ rb_sysopen - output/ttl/relation/chembl_compound-chembl_target.ttl (Errno::EACCES) from /data/togoid/git/togoid-config/lib/togoid-config.rb:237:in `open' From 8b9d7adba40aa3385d49f2b34c5719d0b532f690 Mon Sep 17 00:00:00 2001 From: sh-ikeda Date: Mon, 23 Dec 2024 11:49:39 +0900 Subject: [PATCH 4/6] add description to suggest another path --- config/bioproject-biosample/config.yaml | 1 + config/biosample-bioproject/config.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/config/bioproject-biosample/config.yaml b/config/bioproject-biosample/config.yaml index e8e2115e..5d18d84b 100644 --- a/config/bioproject-biosample/config.yaml +++ b/config/bioproject-biosample/config.yaml @@ -2,6 +2,7 @@ link: file: sample.tsv forward: TIO_000094 reverse: TIO_000095 + description: "The relationship between BioSample and BioProject is derived from the XML files provided by BioSample (biosample_set.xml) and BioProject (bioproject.xml). However, these files do not comprehensively cover all relations. If you are unable to find direct relations between your input BioSample/BioProject IDs and the corresponding BioProject/BioSample IDs, please consider using the path via SRA Experiment IDs, which may contains expected relations." update: frequency: Monthly method: awk -F "\t" 'FNR==1{fn++} fn==1{b[$1,$2]=1; print $1 "\t" $2} fn==2&&$2=="ID"{a[$3]=$1} fn==3&&$2=="BioProject ID"&&a[$3]&&!b[a[$3],$1]{print a[$3] "\t" $1}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv diff --git a/config/biosample-bioproject/config.yaml b/config/biosample-bioproject/config.yaml index c6324faf..8d89f8de 100644 --- a/config/biosample-bioproject/config.yaml +++ b/config/biosample-bioproject/config.yaml @@ -2,6 +2,7 @@ link: file: sample.tsv forward: TIO_000095 reverse: TIO_000094 + description: "The relationship between BioSample and BioProject is derived from the XML files provided by BioSample (biosample_set.xml) and BioProject (bioproject.xml). However, these files do not comprehensively cover all relations. If you are unable to find direct relations between your input BioSample/BioProject IDs and the corresponding BioProject/BioSample IDs, please consider using the path via SRA Experiment IDs, which may contains expected relations." update: frequency: Monthly method: awk -F "\t" 'FNR==1{fn++} fn==1{b[$2,$1]=1; print $2 "\t" $1} fn==2&&$2=="ID"{a[$3]=$1} fn==3&&$2=="BioProject ID"&&a[$3]&&!b[$1,a[$3]]{print $1 "\t" a[$3]}' $TOGOID_ROOT/input/bioproject/bioproject2biosample.tsv $TOGOID_ROOT/input/bioproject/bioproject.tsv $TOGOID_ROOT/input/biosample/biosample_set.tsv From 4a19910dcb3e09648ed93df4dda171fc59ba4c62 Mon Sep 17 00:00:00 2001 From: sh-ikeda Date: Mon, 23 Dec 2024 11:51:59 +0900 Subject: [PATCH 5/6] weekly update --- docs/help.md | 4 ++-- docs/help_ja.md | 4 ++-- docs/news.md | 3 +++ 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/docs/help.md b/docs/help.md index 485f4458..05ce5757 100644 --- a/docs/help.md +++ b/docs/help.md @@ -1,5 +1,5 @@ # TogoID ver. 2.0 -Datasets last updated: 2024-12-17 +Datasets last updated: 2024-12-23 ## About - [TogoID](https://togoid.dbcls.jp/) is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an [ontology](https://togoid.dbcls.jp/ontology) that defines the semantics of the dataset relations. @@ -10,7 +10,7 @@ Datasets last updated: 2024-12-17 ## Video tutorial - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8) -## Statistics (as of 2024-12-17) +## Statistics (as of 2024-12-23) - Number of target datasets - 105 (from 73 databases) - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. diff --git a/docs/help_ja.md b/docs/help_ja.md index d3e90ffe..694c3c94 100644 --- a/docs/help_ja.md +++ b/docs/help_ja.md @@ -1,5 +1,5 @@ # TogoID ver. 2.0 -Datasets last updated: 2024-12-17 +Datasets last updated: 2024-12-23 ## About - [TogoID](https://togoid.dbcls.jp/) は、直感的なインターフェースにより生命科学系データベース(DB)間のつながりを探索的に確認しながらID変換を行うことができるウェブアプリケーションです。同一の実体を指すID間の変換だけでなく、関連する別のカテゴリーのIDへの変換も可能です。また、直接リンクされていないDBのID間でも、他のDBを経由した変換を探索することができます。 @@ -10,7 +10,7 @@ Datasets last updated: 2024-12-17 ## 動画マニュアル - [TogoIDを使って生命科学系データベースのさまざまなIDを探索的に変換する](https://youtu.be/gXnvm6Fn4R8) -## 統計 (2024-12-17) +## 統計 (2024-12-23) - 対象データセット数 - 105 (73 のデータベースに由来) - 対象DBの詳細やID例については、"DATASETS" タブ からご覧いただけます。 diff --git a/docs/news.md b/docs/news.md index 3753afdb..7499bfb0 100644 --- a/docs/news.md +++ b/docs/news.md @@ -1,3 +1,6 @@ +# 2024-12-23 +- Weekly update has been completed. + # 2024-12-17 - Weekly update has been completed. From 70f8e49cf0fee9be01324bba937b228678118980 Mon Sep 17 00:00:00 2001 From: sh-ikeda Date: Mon, 23 Dec 2024 11:55:26 +0900 Subject: [PATCH 6/6] update curl version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ea4bfe7e..6988cb07 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,7 +6,7 @@ RUN apt-get update -y && apt-get install -y \ libjson-perl=4.04000-1 \ libany-uri-escape-perl=0.01-3 \ libwww-perl=6.61-1 \ - curl=7.81.0-1ubuntu1.19 \ + curl=7.81.0-1ubuntu1.20 \ wget=1.21.2-2ubuntu1 \ gawk=1:5.1.0-1build3 \ python3=3.10.6-1~22.04.1 \