diff --git a/docs/help.md b/docs/help.md
index 6b051ddd..485f4458 100644
--- a/docs/help.md
+++ b/docs/help.md
@@ -1,5 +1,5 @@
# TogoID ver. 2.0
-Datasets last updated: 2024-12-09
+Datasets last updated: 2024-12-17
## 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: 2024-12-09
## Video tutorial
- [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
-## Statistics (as of 2024-12-09)
+## Statistics (as of 2024-12-17)
- 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 bb9363c2..d3e90ffe 100644
--- a/docs/help_ja.md
+++ b/docs/help_ja.md
@@ -1,5 +1,5 @@
# TogoID ver. 2.0
-Datasets last updated: 2024-12-09
+Datasets last updated: 2024-12-17
## 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: 2024-12-09
## 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 (2024-12-09)
+## 統計 (2024-12-17)
- 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 ea6e5223..3753afdb 100644
--- a/docs/news.md
+++ b/docs/news.md
@@ -1,8 +1,5 @@
-# *NOTICE*
-Some of the features of TogoID will be temporarily unavailable due to our system maintenance from 09:00 on December 13, 2024, to 18:00 on December 16, 2024 (JST).
-The *LABEL2ID* function will not be available, and the *label display features* for some datasets will also be affected.
-The *ID-to-ID conversion function will remain available* as usual throughout the maintenance period.
-We apologize for any incovenience caused.
+# 2024-12-17
+- Weekly update has been completed.
# 2024-12-09
- Weekly update has been completed.
diff --git a/log/config-summary.tsv b/log/config-summary.tsv
index 61131f17..1746c702 100644
--- a/log/config-summary.tsv
+++ b/log/config-summary.tsv
@@ -72,7 +72,7 @@ hgnc-ncbigene nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00073 Gene NC
hgnc-omim_gene nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00154 Gene OMIM gene http://identifiers.org/mim/ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$32{gsub(\"\\\"\",\"\",$32); split($32,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-pubmed nbdc01774 Gene HGNC http://identifiers.org/hgnc/ 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 Bimonthly "awk -F \"\\t\" 'FNR>=2&&$27{gsub(\"\\\"\",\"\",$27); split($27,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-refseq_genomic nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Gene RefSeq genomic http://identifiers.org/refseq/ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
-hgnc-refseq_rna nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Transcript RefSeq RNA http://identifiers.org/refseq/ tio:TIO_000035 gene is transcribed to transcript is transcribed to tio:TIO_000034 transcript is transcribed from gene is transcribed from Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-refseq_rna nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Transcript RefSeq RNA http://identifiers.org/refseq/ tio:TIO_000035 gene is transcribed to transcript is transcribed to tio:TIO_000034 transcript is transcribed from gene is transcribed from Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" gensub(/\\.$/,\"\",\"g\",a[k])}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-rgd nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00188 Gene RGD http://identifiers.org/rgd/ tio:TIO_000017 sequence is orthologous to sequence is orthologous to tio:TIO_000017 sequence is orthologous to sequence is orthologous to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$29{gsub(\"\\\"\",\"\",$29); split($29,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-uniprot nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00221 Protein UniProt http://purl.uniprot.org/uniprot/ tio:TIO_000025 gene has protein as product has gene product tio:TIO_000024 protein is product of gene is product of gene Bimonthly "awk -F \"\\t\" 'FNR>=2&&$26{gsub(\"\\\"\",\"\",$26); split($26,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hmdb-chebi nbdc00909 Compound HMDB http://identifiers.org/hmdb/ nbdc00027 Compound ChEBI compound http://purl.obolibrary.org/obo/CHEBI_ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Triennial "awk -F \"\\t\" '$2==\"chebi_id\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/hmdb/hmdb_metabolites.tsv"
diff --git a/log/error.log b/log/error.log
index 1f90dd44..2be106fc 100644
--- a/log/error.log
+++ b/log/error.log
@@ -1,13 +1,72 @@
-Error: download_file(input/glytoucan, https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv): Command failed with status (8): [wget --quiet --recursive --no-parent --no-...]
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 1538 / 4376 = 0.35146252285191953 < 0.5
+# 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
@@ -63,46 +122,4 @@ Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/pa
# Error: Failed to create output/tsv/mondo-omim_phenotype.tsv or created file was empty
# 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
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv new file size per old 291 / 385314 = 0.0007552282034911786 < 0.5
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML 408 Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Server timeout waiting for the HTTP request from the client.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Additionally a 502 Bad Gateway
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML 408 Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Server timeout waiting for the HTTP request from the client.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Additionally a 502 Bad Gateway
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/togovar-ensembl_transcript.tsv new file size per old 0 / 8069270901 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-ensembl_transcript.tsv or created file was empty
-# Error: output/tsv/togovar-ncbigene.tsv new file size per old 0 / 1097267175 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-ncbigene.tsv or created file was empty
-# Error: output/tsv/togovar-pubmed.tsv new file size per old 0 / 14408635 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-pubmed.tsv or created file was empty
-# Error: output/tsv/togovar-refseq_rna.tsv new file size per old 0 / 4180808277 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-refseq_rna.tsv or created file was empty
-# Error: output/tsv/uberon-ncit_tissue.tsv new file size per old 288 / 38722 = 0.007437632353700738 < 0.5
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML 502 Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server received an invalid
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request
Reason: Error reading from remote server
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML 502 Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server received an invalid
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request
Reason: Error reading from remote server
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 60240 / 470542 = 0.12802257821830995 < 0.5
diff --git a/log/pair_count.tsv b/log/pair_count.tsv
index 34c2a617..93965b12 100644
--- a/log/pair_count.tsv
+++ b/log/pair_count.tsv
@@ -3,11 +3,11 @@ assembly_insdc-bioproject.tsv 2283159
assembly_insdc-biosample.tsv 2225812
assembly_insdc-insdc_master.tsv 2150193
bioproject-biosample.tsv 2546485
-bioproject-geo_series.tsv 221334
-bioproject-pubmed.tsv 282694
+bioproject-geo_series.tsv 221856
+bioproject-pubmed.tsv 283298
bioproject_umbrella-bioproject.tsv 104586
-biosample-bioproject.tsv 20439564
-biosample-geo_sample.tsv 9573846
+biosample-bioproject.tsv 20508479
+biosample-geo_sample.tsv 9590138
cellosaurus-ncit_disease.tsv 75821
cellosaurus-orphanet_phenotype.tsv 41448
chebi-glytoucan.tsv 10615
@@ -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 2937889
-clinvar-hgnc.tsv 3068652
-clinvar-medgen.tsv 4210198
-clinvar-mondo.tsv 2001160
-clinvar-ncbigene.tsv 3068972
-clinvar-omim_phenotype.tsv 1646702
-clinvar-orphanet_phenotype.tsv 1871572
+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-uniprot.tsv 20800
cog-insdc.tsv 115826
cog-refseq_protein.tsv 3340026
@@ -66,18 +66,18 @@ glytoucan-ncbigene.tsv 1270
glytoucan-uniprot-TIO_000060.tsv 82906
glytoucan-uniprot-TIO_000126.tsv 402
glytoucan-uniprot-TIO_000128.tsv 310
-glytoucan-uniprot.tsv 82906
+glytoucan-uniprot.tsv 70216
hgnc-ccds.tsv 35510
hgnc-ec.tsv 2121
hgnc-ensembl_gene.tsv 41201
hgnc-hgnc_symbol.tsv 43839
hgnc-insdc.tsv 21140
hgnc-lrg.tsv 1325
-hgnc-mgi_gene.tsv 24077
+hgnc-mgi_gene.tsv 24078
hgnc-mirbase.tsv 1912
hgnc-ncbigene.tsv 43753
-hgnc-omim_gene.tsv 17348
-hgnc-pubmed.tsv 35052
+hgnc-omim_gene.tsv 17350
+hgnc-pubmed.tsv 35060
hgnc-refseq_genomic.tsv 13532
hgnc-refseq_rna.tsv 28712
hgnc-rgd.tsv 18945
@@ -87,10 +87,10 @@ hmdb-inchi_key.tsv 217899
hmdb-pdb_ccd.tsv 522
hmdb-pubchem_compound.tsv 104230
homologene-ncbigene.tsv 275237
-hp_inheritance-omim_phenotype.tsv 8814
+hp_inheritance-omim_phenotype.tsv 8823
hp_phenotype-ncbigene.tsv 220065
-hp_phenotype-omim_phenotype.tsv 137689
-hp_phenotype-orphanet_phenotype.tsv 113135
+hp_phenotype-omim_phenotype.tsv 139028
+hp_phenotype-orphanet_phenotype.tsv 114066
insdc-bioproject.tsv 59409158
insdc-biosample.tsv 193975949
insdc_master-bioproject.tsv 1533582
@@ -119,7 +119,7 @@ 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 112132
+mgi_gene-mgi_allele.tsv 112260
mgi_gene-ncbigene.tsv 90618
mgi_gene-uniprot.tsv 79070
mgi_genotype-doid.tsv 7844
@@ -132,26 +132,26 @@ mondo-mesh.tsv 8352
mondo-omim_phenotype.tsv 9693
mondo-orphanet_phenotype.tsv 10380
nando-mondo.tsv 2390
-ncbigene-ensembl_gene.tsv 11788732
-ncbigene-ensembl_protein.tsv 13562026
-ncbigene-ensembl_transcript.tsv 14257155
+ncbigene-ensembl_gene.tsv 11755401
+ncbigene-ensembl_protein.tsv 13509818
+ncbigene-ensembl_transcript.tsv 14158040
ncbigene-flybase_gene.tsv 25078
-ncbigene-go.tsv 102596805
+ncbigene-go.tsv 102800883
ncbigene-hgnc.tsv 43859
ncbigene-mgi_gene.tsv 71682
ncbigene-mirbase.tsv 17541
-ncbigene-omim_gene.tsv 18559
-ncbigene-refseq_genomic.tsv 211769
-ncbigene-refseq_protein.tsv 69806245
-ncbigene-refseq_rna.tsv 67710490
+ncbigene-omim_gene.tsv 18562
+ncbigene-refseq_genomic.tsv 211772
+ncbigene-refseq_protein.tsv 69891186
+ncbigene-refseq_rna.tsv 67763645
ncbigene-rgd.tsv 77241
ncbigene-sgd.tsv 6471
ncbigene-tair.tsv 32835
-ncbigene-taxonomy.tsv 57866358
+ncbigene-taxonomy.tsv 57932960
ncbigene-vgnc.tsv 112163
ncbigene-wormbase_gene.tsv 28785
ncbigene-xenbase_gene.tsv 46840
-ncbigene-zfin_gene.tsv 27178
+ncbigene-zfin_gene.tsv 27181
ncit_disease-ncit_tissue.tsv 27199
oma_protein-ensembl_gene.tsv 2533621
oma_protein-ensembl_transcript.tsv 2925554
@@ -170,32 +170,32 @@ pdb-interpro.tsv 726658
pdb-pdb_ccd.tsv 530587
pdb-pfam.tsv 339565
pdb-uniprot.tsv 341431
-pmc-pubmed.tsv 9703036
+pmc-pubmed.tsv 9722361
prosite-prosite_prorule.tsv 1459
pubchem_compound-atc.tsv 4965
pubchem_compound-chebi.tsv 174843
pubchem_compound-chembl_compound.tsv 2372556
pubchem_compound-drugbank.tsv 10789
pubchem_compound-glytoucan.tsv 69203
-pubchem_compound-inchi_key.tsv 119107534
+pubchem_compound-inchi_key.tsv 119108895
pubchem_pathway-ncbigene.tsv 33861
pubchem_pathway-pathbank.tsv 69387
pubchem_pathway-pubchem_compound.tsv 1253395
pubchem_pathway-reactome_pathway.tsv 2877
pubchem_pathway-uniprot.tsv 623594
pubchem_pathway-wikipathways.tsv 1267
-reactome_pathway-chebi.tsv 270070
+reactome_pathway-chebi.tsv 270398
reactome_pathway-go.tsv 13144
reactome_pathway-iuphar_ligand.tsv 41304
reactome_pathway-mirbase.tsv 348
reactome_pathway-reactome_reaction.tsv 393545
-reactome_pathway-uniprot.tsv 868219
-reactome_reaction-chebi.tsv 203666
+reactome_pathway-uniprot.tsv 871849
+reactome_reaction-chebi.tsv 204183
reactome_reaction-go.tsv 3318
reactome_reaction-iuphar_ligand.tsv 14709
reactome_reaction-mirbase.tsv 194
-reactome_reaction-uniprot.tsv 679876
-refseq_protein-uniprot.tsv 159946382
+reactome_reaction-uniprot.tsv 683457
+refseq_protein-uniprot.tsv 175209073
refseq_rna-dbsnp.tsv 267033326
refseq_rna-hgnc.tsv 227308
refseq_rna-ncbigene.tsv 66957414
@@ -209,28 +209,28 @@ rhea-go.tsv 4448
rhea-pubmed.tsv 142680
rhea-reactome_reaction.tsv 1511
rhea-uniprot.tsv 42384671
-sra_accession-bioproject.tsv 543090
-sra_accession-biosample.tsv 32388968
+sra_accession-bioproject.tsv 543595
+sra_accession-biosample.tsv 32427001
sra_accession-sra_analysis.tsv 329302
-sra_accession-sra_experiment.tsv 36430485
-sra_accession-sra_project.tsv 629932
-sra_accession-sra_run.tsv 41251239
-sra_accession-sra_sample.tsv 35118028
-sra_experiment-bioproject.tsv 31918768
-sra_experiment-biosample.tsv 32226084
-sra_experiment-sra_project.tsv 32263289
-sra_experiment-sra_sample.tsv 32263012
-sra_project-bioproject.tsv 543109
-sra_run-bioproject.tsv 33803917
-sra_run-biosample.tsv 34126791
-sra_run-sra_experiment.tsv 34170279
-sra_run-sra_project.tsv 34161212
-sra_run-sra_sample.tsv 34163744
-sra_sample-biosample.tsv 32403387
+sra_accession-sra_experiment.tsv 36544800
+sra_accession-sra_project.tsv 632118
+sra_accession-sra_run.tsv 41367694
+sra_accession-sra_sample.tsv 35257303
+sra_experiment-bioproject.tsv 31968733
+sra_experiment-biosample.tsv 32265671
+sra_experiment-sra_project.tsv 32313254
+sra_experiment-sra_sample.tsv 32312977
+sra_project-bioproject.tsv 543614
+sra_run-bioproject.tsv 33855800
+sra_run-biosample.tsv 34166458
+sra_run-sra_experiment.tsv 34222772
+sra_run-sra_project.tsv 34213095
+sra_run-sra_sample.tsv 34213846
+sra_sample-biosample.tsv 32441420
swisslipids-chebi.tsv 4276
swisslipids-hmdb.tsv 26026
swisslipids-inchi_key.tsv 593209
-taxonomy-pubmed.tsv 50709
+taxonomy-pubmed.tsv 50715
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 5303878533
+total 5320359597
diff --git a/log/pair_count_history.tsv b/log/pair_count_history.tsv
index 76c06ac6..e26eedfb 100644
--- a/log/pair_count_history.tsv
+++ b/log/pair_count_history.tsv
@@ -68,3 +68,4 @@ Date affy_probeset-ncbigene assembly_insdc-bioproject assembly_insdc-biosample a
2024-11-23 19063 2283159 2225812 2150193 2546485 220473 281950 104586 20329479 9540054 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 2937841 3061979 4196850 1993860 3062299 1639794 1865790 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 2118 41199 43838 21140 1325 24072 1912 43753 17339 35030 13532 28712 18945 20374 13701 217899 522 104230 275237 8814 220065 137689 113135 59409158 193975949 1533582 1533178 30282 1645155 21310 1282 114937 477238 1274 770832917 199 305 130 12929 48152 12349 137319849 6318 16674 16849 21567 7229 11043 9063 56426 24584 112050 90618 79070 7840 125052 401482 10712 574 1486 8352 9693 10380 2390 11681986 13454144 14146143 25078 102598546 43845 71682 17541 18551 211770 69690608 67642626 77241 6471 32835 57768578 112162 28785 46840 27177 27199 2533621 2925554 5849918 14432954 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 9664384 1455 4965 174843 2372556 10789 69203 119096713 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 4435 142680 1511 41448659 537619 32063559 329284 36134714 625496 40945774 34837349 31577033 31881755 31921554 31921277 537638 33463976 33772350 33847764 33821271 33813940 32077978 4276 26026 593209 50616 745335 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10336 66728 41313492 9613808 9834392 9834392 532822218 82524 264947440 237103 12855457 7617387 16357 7263 7981 390829 282944 45329880 248838887 248838887 641755 191 698680 5929 1153 4131 1429 30267 33518 5199738167
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
diff --git a/log/update.log b/log/update.log
index 8f8ee95d..93043c15 100644
--- a/log/update.log
+++ b/log/update.log
@@ -1,16 +1,16 @@
-*** Started: 2024-12-06T17:00:15 ***
+*** Started: 2024-12-15T21:57:19 ***
## Prepare input files for BioProject
# Checking lock file input/bioproject/download.lock for download
-# Local file time: 2024-11-28 19:15:01 +0900 (input/bioproject/bioproject.xml)
-# Remote file time: 2024-12-05 10:34:50 +0000 (https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml)
+# 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)
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
# 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: 2024-11-28 23:34:28 +0900 (input/biosample/biosample_set.xml.gz)
-# Remote file time: 2024-12-05 15:27:18 +0000 (https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz)
+# 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)
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
@@ -24,20 +24,18 @@ python bin/biosample_xml2tsv.py input/biosample/biosample_set.xml > input/biosam
# Preserving timestamp of the input/cellosaurus/download.lock
## Prepare input files for ClinVar
# Checking lock file input/clinvar/download.lock for download
-# Local file time: 2024-11-27 02:55:50 +0900 (input/clinvar/variant_summary.txt.gz)
-# Remote file time: 2024-12-01 19:53:33 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz)
+# 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)
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 6.998066154460151 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
+# 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
## 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
-Error: download_file(input/glytoucan, https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv): Command failed with status (8): [wget --quiet --recursive --no-parent --no-...]
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
## Prepare input files for HMDB
@@ -49,8 +47,8 @@ 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: 2024-11-27 00:28:00 +0900 (input/hgnc/hgnc_complete_set.txt)
-# Remote file time: 2024-12-03 13:35:33 +0000 (https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt)
+# Local file time: 2024-12-03 22:35:33 +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
## Prepare input files for Homologene
@@ -63,15 +61,13 @@ Error: Remote file is empty
## 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)
-# Remote file time: 2024-08-13 12:11:36 +0000 (http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa)
-# Local file size: 33207148 (input/hp_phenotype/phenotype.hpoa)
-# Remote file size: 33207148 (http://purl.obolibrary.org/obo/hp/hpoa/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)
-# Remote file time: 2024-08-13 12:11:09 +0000 (http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt)
-# Local file size: 19507647 (input/hp_phenotype/genes_to_phenotype.txt)
-# Remote file size: 19507647 (http://purl.obolibrary.org/obo/hp/hpoa/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
bin/sparql_csv2tsv.sh bin/sparql/hp_category.rq https://rdfportal.org/bioportal/sparql > input/hp_phenotype/hp_category.tsv
-# Preserving timestamp of the input/hp_phenotype/download.lock
+# Overwriting 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)
@@ -101,53 +97,48 @@ bin/sparql_csv2tsv.sh bin/sparql/hp_category.rq https://rdfportal.org/bioportal/
## 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: 2024-11-25 13:03:48 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt)
-# Local file size: 87585919 (input/mgi_gene/MRK_List2.rpt)
-# Remote file size: 87585919 (https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt)
+# Remote file time: 2024-12-09 13:01:37 +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: 2024-11-25 13:01:48 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_Gene_Model_Coord.rpt)
-# Local file size: 14028801 (input/mgi_gene/MGI_Gene_Model_Coord.rpt)
-# Remote file size: 14028801 (https://www.informatics.jax.org/downloads/reports/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)
+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: 2024-11-25 13:03:58 +0000 (https://www.informatics.jax.org/downloads/reports/MRK_SwissProt_TrEMBL.rpt)
-# Local file size: 2103266 (input/mgi_gene/MRK_SwissProt_TrEMBL.rpt)
-# Remote file size: 2103266 (https://www.informatics.jax.org/downloads/reports/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)
+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: 2024-11-25 13:00:44 +0000 (https://www.informatics.jax.org/downloads/reports/HGNC_AllianceHomology.rpt)
-# Local file size: 11343240 (input/mgi_gene/HGNC_AllianceHomology.rpt)
-# Remote file size: 11343240 (https://www.informatics.jax.org/downloads/reports/HGNC_AllianceHomology.rpt)
+# Remote file time: 2024-12-09 13:00:26 +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: 2024-11-25 13:03:10 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_PhenotypicAllele.rpt)
-# Local file size: 25646822 (input/mgi_gene/MGI_PhenotypicAllele.rpt)
-# Remote file size: 25646822 (https://www.informatics.jax.org/downloads/reports/MGI_PhenotypicAllele.rpt)
-# Preserving timestamp of the input/mgi_gene/download.lock
+# Remote file time: 2024-12-09 13:01:17 +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: 2024-11-25 13:01:31 +0000 (https://www.informatics.jax.org/downloads/reports/MGI_DiseaseGeneModel.rpt)
-# Local file size: 14058439 (input/mgi_genotype/MGI_DiseaseGeneModel.rpt)
-# Remote file size: 14058439 (https://www.informatics.jax.org/downloads/reports/MGI_DiseaseGeneModel.rpt)
-# Preserving timestamp of the input/mgi_genotype/download.lock
+# Remote file time: 2024-12-09 13:00:42 +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: 2024-11-28 15:56:00 +0900 (input/ncbigene/gene2refseq.gz)
-# Remote file time: 2024-12-05 12:27:37 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz)
+# 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)
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: 2024-11-28 15:51:22 +0900 (input/ncbigene/gene2ensembl.gz)
-# Remote file time: 2024-12-05 12:22:59 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz)
+# 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)
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: 2024-11-28 15:53:04 +0900 (input/ncbigene/gene2go.gz)
-# Remote file time: 2024-12-05 12:24:42 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz)
+# 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)
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: 2024-11-28 16:03:20 +0900 (input/ncbigene/Homo_sapiens.gene_info.gz)
-# Remote file time: 2024-12-05 12:34:46 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz)
+# 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)
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: 2024-11-28 15:57:52 +0900 (input/ncbigene/gene_info.gz)
-# Remote file time: 2024-12-05 12:29:36 +0000 (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz)
+# 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)
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
@@ -168,8 +159,8 @@ 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: 2024-11-29 19:21:14 +0900 (input/pmc/PMC-ids.csv.gz)
-# Remote file time: 2024-12-06 10:11:57 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz)
+# 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)
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
@@ -187,58 +178,46 @@ gzip -dc input/pmc/PMC-ids.csv.gz > input/pmc/PMC-ids.csv
## 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)
-# Remote file time: 2024-09-29 02:50:03 +0000 (https://reactome.org/download/current/UniProt2ReactomeReactions.txt)
-# Local file size: 95628484 (input/reactome/UniProt2ReactomeReactions.txt)
-# Remote file size: 95628484 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 02:50:56 +0000 (https://reactome.org/download/current/ChEBI2ReactomeReactions.txt)
-# Local file size: 28722869 (input/reactome/ChEBI2ReactomeReactions.txt)
-# Remote file size: 28722869 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:10:03 +0000 (https://reactome.org/download/current/Ensembl2ReactomeReactions.txt)
-# Local file size: 423004134 (input/reactome/Ensembl2ReactomeReactions.txt)
-# Remote file size: 423004134 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:13:26 +0000 (https://reactome.org/download/current/miRBase2ReactomeReactions.txt)
-# Local file size: 27061 (input/reactome/miRBase2ReactomeReactions.txt)
-# Remote file size: 27061 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:13:22 +0000 (https://reactome.org/download/current/NCBI2ReactomeReactions.txt)
-# Local file size: 72461893 (input/reactome/NCBI2ReactomeReactions.txt)
-# Remote file size: 72461893 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:13:35 +0000 (https://reactome.org/download/current/GtoP2ReactomeReactions.txt)
-# Local file size: 1868064 (input/reactome/GtoP2ReactomeReactions.txt)
-# Remote file size: 1868064 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 02:49:33 +0000 (https://reactome.org/download/current/UniProt2Reactome_All_Levels.txt)
-# Local file size: 108121376 (input/reactome/UniProt2Reactome_All_Levels.txt)
-# Remote file size: 108121376 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 02:50:50 +0000 (https://reactome.org/download/current/ChEBI2Reactome_All_Levels.txt)
-# Local file size: 33100943 (input/reactome/ChEBI2Reactome_All_Levels.txt)
-# Remote file size: 33100943 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:07:44 +0000 (https://reactome.org/download/current/Ensembl2Reactome_All_Levels.txt)
-# Local file size: 460980583 (input/reactome/Ensembl2Reactome_All_Levels.txt)
-# Remote file size: 460980583 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:13:25 +0000 (https://reactome.org/download/current/miRBase2Reactome_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)
+# 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)
-# Remote file time: 2024-09-29 03:12:58 +0000 (https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt)
-# Local file size: 81212675 (input/reactome/NCBI2Reactome_All_Levels.txt)
-# Remote file size: 81212675 (https://reactome.org/download/current/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)
-# Remote file time: 2024-09-29 03:13:33 +0000 (https://reactome.org/download/current/GtoP2Reactome_All_Levels.txt)
-# Local file size: 4817918 (input/reactome/GtoP2Reactome_All_Levels.txt)
-# Remote file size: 4817918 (https://reactome.org/download/current/GtoP2Reactome_All_Levels.txt)
-# Preserving timestamp of the input/reactome/download.lock
+# 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
## Prepare input files for RefSeq Protein
# Checking lock file input/refseq_protein/download.lock for download
-# Local file time: 2024-11-28 19:22:48 +0900 (input/refseq_protein/gene_refseq_uniprotkb_collab.gz)
-# Remote file time: 2024-12-05 10:23:44 +0000 (https://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz)
+# 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)
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
@@ -265,8 +244,8 @@ 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: 2024-11-29 00:57:33 +0900 (input/sra/SRA_Accessions.tab)
-# Remote file time: 2024-12-05 16:08:41 +0000 (https://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab)
+# 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)
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
@@ -290,103 +269,132 @@ 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: 2024-11-29 21:28:38 +0900 (input/taxonomy/taxdump.tar.gz)
-# Remote file time: 2024-12-06 10:29:01 +0000 (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz)
+# 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)
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 6.9274939552590284 days ago (will be updated when >5 days)
+# File output/tsv/affy_probeset-ncbigene.tsv is created 9.217587901309283 days ago (will be updated when >5 days)
## Update config/affy_probeset-ncbigene/config.yaml => output/tsv/affy_probeset-ncbigene.tsv
-< 2024-12-06T19:52:55 affy_probeset-ncbigene
+< 2024-12-16T01:06:15 affy_probeset-ncbigene
togoid-config config/affy_probeset-ncbigene update
-# Success: output/tsv/affy_probeset-ncbigene.tsv is updated
-> 2024-12-06T19:52:56 affy_probeset-ncbigene
+# 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
Rule for TSV (output/tsv/affy_probeset-ncbigene.tsv)
------------------------------
Investigating output/tsv/affy_probeset-ncbigene.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 19:52:56 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.92747796173919 days ago (will be updated when >5 days)
+# File output/tsv/assembly_insdc-bioproject.tsv is created 9.217571553977534 days ago (will be updated when >5 days)
## Update config/assembly_insdc-bioproject/config.yaml => output/tsv/assembly_insdc-bioproject.tsv
-< 2024-12-06T19:52:56 assembly_insdc-bioproject
+< 2024-12-16T01:06:16 assembly_insdc-bioproject
togoid-config config/assembly_insdc-bioproject update
-# Success: output/tsv/assembly_insdc-bioproject.tsv is updated
-> 2024-12-06T19:52:58 assembly_insdc-bioproject
+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
Rule for TSV (output/tsv/assembly_insdc-bioproject.tsv)
------------------------------
Investigating output/tsv/assembly_insdc-bioproject.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 19:52:58 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.927477433173334 days ago (will be updated when >5 days)
+# File output/tsv/assembly_insdc-biosample.tsv is created 9.219019775532976 days ago (will be updated when >5 days)
## Update config/assembly_insdc-biosample/config.yaml => output/tsv/assembly_insdc-biosample.tsv
-< 2024-12-06T19:52:58 assembly_insdc-biosample
+< 2024-12-16T01:08:24 assembly_insdc-biosample
togoid-config config/assembly_insdc-biosample update
-# Success: output/tsv/assembly_insdc-biosample.tsv is updated
-> 2024-12-06T19:53:01 assembly_insdc-biosample
+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
Rule for TSV (output/tsv/assembly_insdc-biosample.tsv)
------------------------------
Investigating output/tsv/assembly_insdc-biosample.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 19:53:01 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.927476156654213 days ago (will be updated when >5 days)
+# File output/tsv/assembly_insdc-insdc_master.tsv is created 9.220466882386042 days ago (will be updated when >5 days)
## Update config/assembly_insdc-insdc_master/config.yaml => output/tsv/assembly_insdc-insdc_master.tsv
-< 2024-12-06T19:53:01 assembly_insdc-insdc_master
+< 2024-12-16T01:10:31 assembly_insdc-insdc_master
togoid-config config/assembly_insdc-insdc_master update
-# Success: output/tsv/assembly_insdc-insdc_master.tsv is updated
-> 2024-12-06T19:53:03 assembly_insdc-insdc_master
+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
Rule for TSV (output/tsv/assembly_insdc-insdc_master.tsv)
------------------------------
Investigating output/tsv/assembly_insdc-insdc_master.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 19:53:03 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 config/bioproject-biosample/config.yaml => output/tsv/bioproject-biosample.tsv
-< 2024-12-06T19:53:03 bioproject-biosample
+< 2024-12-16T01:12:39 bioproject-biosample
togoid-config config/bioproject-biosample update
-# Success: output/tsv/bioproject-biosample.tsv is updated
-> 2024-12-06T19:53:06 bioproject-biosample
+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
Rule for TSV (output/tsv/bioproject-biosample.tsv)
------------------------------
Investigating output/tsv/bioproject-biosample.tsv
@@ -395,59 +403,62 @@ task needed: true
timestamp: 2024-12-06 19:53:06 +0900
pre-requisites:
--output/tsv/ ()
---prepare:bioproject (2024-12-06 19:53:06 +0900)
-latest-prerequisite time: 2024-12-06 19:53:06 +0900
+--prepare:bioproject (2024-12-16 01:14:46 +0900)
+latest-prerequisite time: 2024-12-16 01:14:46 +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
-< 2024-12-06T19:53:06 bioproject-geo_series
+< 2024-12-16T01:14:46 bioproject-geo_series
togoid-config config/bioproject-geo_series update
# Success: output/tsv/bioproject-geo_series.tsv is updated
-> 2024-12-06T19:53:08 bioproject-geo_series
+> 2024-12-16T01:14:48 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: 2024-12-06 19:53:08 +0900
+timestamp: 2024-12-16 01:14:48 +0900
pre-requisites:
--output/tsv/ ()
---prepare:bioproject (2024-12-06 19:53:08 +0900)
-latest-prerequisite time: 2024-12-06 19:53:08 +0900
+--prepare:bioproject (2024-12-16 01:14:48 +0900)
+latest-prerequisite time: 2024-12-16 01:14:48 +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
-< 2024-12-06T19:53:08 bioproject-pubmed
+< 2024-12-16T01:14:48 bioproject-pubmed
togoid-config config/bioproject-pubmed update
# Success: output/tsv/bioproject-pubmed.tsv is updated
-> 2024-12-06T19:53:09 bioproject-pubmed
+> 2024-12-16T01:14:50 bioproject-pubmed
Rule for TSV (output/tsv/bioproject-pubmed.tsv)
------------------------------
Investigating output/tsv/bioproject-pubmed.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 19:53:09 +0900
+timestamp: 2024-12-16 01:14:50 +0900
pre-requisites:
--output/tsv/ ()
---prepare:bioproject (2024-12-06 19:53:09 +0900)
-latest-prerequisite time: 2024-12-06 19:53:09 +0900
+--prepare:bioproject (2024-12-16 01:14:50 +0900)
+latest-prerequisite time: 2024-12-16 01:14:50 +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 6.927499172212534 days ago (will be updated when >5 days)
+# File output/tsv/bioproject_umbrella-bioproject.tsv is created 9.223377438290486 days ago (will be updated when >5 days)
## Update config/bioproject_umbrella-bioproject/config.yaml => output/tsv/bioproject_umbrella-bioproject.tsv
-< 2024-12-06T19:53:09 bioproject_umbrella-bioproject
+< 2024-12-16T01:14:50 bioproject_umbrella-bioproject
togoid-config config/bioproject_umbrella-bioproject update
-# Success: output/tsv/bioproject_umbrella-bioproject.tsv is updated
-> 2024-12-06T19:53:10 bioproject_umbrella-bioproject
+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
Rule for TSV (output/tsv/bioproject_umbrella-bioproject.tsv)
------------------------------
Investigating output/tsv/bioproject_umbrella-bioproject.tsv
@@ -456,48 +467,48 @@ task needed: true
timestamp: 2024-12-06 19:53:10 +0900
pre-requisites:
--output/tsv/ ()
---prepare:bioproject (2024-12-06 19:53:10 +0900)
-latest-prerequisite time: 2024-12-06 19:53:10 +0900
+--prepare:bioproject (2024-12-16 01:16:57 +0900)
+latest-prerequisite time: 2024-12-16 01:16:57 +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 config/biosample-bioproject/config.yaml => output/tsv/biosample-bioproject.tsv
-< 2024-12-06T19:53:10 biosample-bioproject
+< 2024-12-16T01:16:57 biosample-bioproject
togoid-config config/biosample-bioproject update
# Success: output/tsv/biosample-bioproject.tsv is updated
-> 2024-12-06T19:55:31 biosample-bioproject
+> 2024-12-16T01:18:21 biosample-bioproject
Rule for TSV (output/tsv/biosample-bioproject.tsv)
------------------------------
Investigating output/tsv/biosample-bioproject.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 19:55:31 +0900
+timestamp: 2024-12-16 01:18:21 +0900
pre-requisites:
--output/tsv/ ()
---prepare:biosample (2024-12-06 19:55:31 +0900)
-latest-prerequisite time: 2024-12-06 19:55:31 +0900
+--prepare:biosample (2024-12-16 01:18:21 +0900)
+latest-prerequisite time: 2024-12-16 01:18:21 +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
-< 2024-12-06T19:55:31 biosample-geo_sample
+< 2024-12-16T01:18:21 biosample-geo_sample
togoid-config config/biosample-geo_sample update
# Success: output/tsv/biosample-geo_sample.tsv is updated
-> 2024-12-06T19:57:07 biosample-geo_sample
+> 2024-12-16T01:19:56 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: 2024-12-06 19:57:07 +0900
+timestamp: 2024-12-16 01:19:56 +0900
pre-requisites:
--output/tsv/ ()
---prepare:biosample (2024-12-06 19:57:07 +0900)
-latest-prerequisite time: 2024-12-06 19:57:07 +0900
+--prepare:biosample (2024-12-16 01:19:56 +0900)
+latest-prerequisite time: 2024-12-16 01:19:56 +0900
................................
### Update TSV for cellosaurus-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -512,8 +523,8 @@ task needed: true
timestamp: 2024-09-13 20:46:20 +0900
pre-requisites:
--output/tsv/ ()
---prepare:cellosaurus (2024-12-06 19:57:07 +0900)
-latest-prerequisite time: 2024-12-06 19:57:07 +0900
+--prepare:cellosaurus (2024-12-16 01:19:56 +0900)
+latest-prerequisite time: 2024-12-16 01:19:56 +0900
................................
### Update TSV for cellosaurus-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -528,271 +539,271 @@ task needed: true
timestamp: 2024-09-13 20:46:24 +0900
pre-requisites:
--output/tsv/ ()
---prepare:cellosaurus (2024-12-06 19:57:07 +0900)
-latest-prerequisite time: 2024-12-06 19:57:07 +0900
+--prepare:cellosaurus (2024-12-16 01:19:56 +0900)
+latest-prerequisite time: 2024-12-16 01:19:56 +0900
................................
### Update TSV for chebi-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.9281628997626035 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T19:57:07 chebi-glytoucan
+< 2024-12-16T01:19:56 chebi-glytoucan
togoid-config config/chebi-glytoucan update
# Success: output/tsv/chebi-glytoucan.tsv is updated
-> 2024-12-06T19:57:08 chebi-glytoucan
+> 2024-12-16T01:19:56 chebi-glytoucan
Rule for TSV (output/tsv/chebi-glytoucan.tsv)
------------------------------
Investigating output/tsv/chebi-glytoucan.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 19:57:08 +0900
+timestamp: 2024-12-16 01:19:56 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chebi-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928160585468715 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T19:57:08 chebi-inchi_key
+< 2024-12-16T01:19:56 chebi-inchi_key
togoid-config config/chebi-inchi_key update
# Success: output/tsv/chebi-inchi_key.tsv is updated
-> 2024-12-06T19:57:09 chebi-inchi_key
+> 2024-12-16T01:19:57 chebi-inchi_key
Rule for TSV (output/tsv/chebi-inchi_key.tsv)
------------------------------
Investigating output/tsv/chebi-inchi_key.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 19:57:09 +0900
+timestamp: 2024-12-16 01:19:57 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928170365695614 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T19:57:09 chembl_compound-chebi
+< 2024-12-16T01:19:57 chembl_compound-chebi
togoid-config config/chembl_compound-chebi update
# Success: output/tsv/chembl_compound-chebi.tsv is updated
-> 2024-12-06T19:57:10 chembl_compound-chebi
+> 2024-12-16T01:19:57 chembl_compound-chebi
Rule for TSV (output/tsv/chembl_compound-chebi.tsv)
------------------------------
Investigating output/tsv/chembl_compound-chebi.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 19:57:10 +0900
+timestamp: 2024-12-16 01:19:57 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-chembl_target if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.917000706496562 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T19:57:10 chembl_compound-chembl_target
+< 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
-> 2024-12-06T20:13:30 chembl_compound-chembl_target
+> 2024-12-16T01:36:09 chembl_compound-chembl_target
Rule for TSV (output/tsv/chembl_compound-chembl_target.tsv)
------------------------------
Investigating output/tsv/chembl_compound-chembl_target.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:30 +0900
+timestamp: 2024-12-16 01:36:09 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928338791680567 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:30 chembl_compound-drugbank
+< 2024-12-16T01:36:09 chembl_compound-drugbank
togoid-config config/chembl_compound-drugbank update
# Success: output/tsv/chembl_compound-drugbank.tsv is updated
-> 2024-12-06T20:13:31 chembl_compound-drugbank
+> 2024-12-16T01:36:10 chembl_compound-drugbank
Rule for TSV (output/tsv/chembl_compound-drugbank.tsv)
------------------------------
Investigating output/tsv/chembl_compound-drugbank.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:31 +0900
+timestamp: 2024-12-16 01:36:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-hmdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928337296978634 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:31 chembl_compound-hmdb
+< 2024-12-16T01:36:10 chembl_compound-hmdb
togoid-config config/chembl_compound-hmdb update
# Success: output/tsv/chembl_compound-hmdb.tsv is updated
-> 2024-12-06T20:13:31 chembl_compound-hmdb
+> 2024-12-16T01:36:10 chembl_compound-hmdb
Rule for TSV (output/tsv/chembl_compound-hmdb.tsv)
------------------------------
Investigating output/tsv/chembl_compound-hmdb.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:31 +0900
+timestamp: 2024-12-16 01:36:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928291782966771 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:31 chembl_compound-inchi_key
+< 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
-> 2024-12-06T20:13:36 chembl_compound-inchi_key
+> 2024-12-16T01:36:14 chembl_compound-inchi_key
Rule for TSV (output/tsv/chembl_compound-inchi_key.tsv)
------------------------------
Investigating output/tsv/chembl_compound-inchi_key.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:36 +0900
+timestamp: 2024-12-16 01:36:14 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928343424493542 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:36 chembl_compound-mesh
+< 2024-12-16T01:36:14 chembl_compound-mesh
togoid-config config/chembl_compound-mesh update
# Success: output/tsv/chembl_compound-mesh.tsv is updated
-> 2024-12-06T20:13:36 chembl_compound-mesh
+> 2024-12-16T01:36:15 chembl_compound-mesh
Rule for TSV (output/tsv/chembl_compound-mesh.tsv)
------------------------------
Investigating output/tsv/chembl_compound-mesh.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:36 +0900
+timestamp: 2024-12-16 01:36:15 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928343117434525 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:36 chembl_compound-pdb_ccd
+< 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
-> 2024-12-06T20:13:37 chembl_compound-pdb_ccd
+> 2024-12-16T01:36:15 chembl_compound-pdb_ccd
Rule for TSV (output/tsv/chembl_compound-pdb_ccd.tsv)
------------------------------
Investigating output/tsv/chembl_compound-pdb_ccd.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:37 +0900
+timestamp: 2024-12-16 01:36:15 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928300555958762 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:37 chembl_compound-pubchem_compound
+< 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
-> 2024-12-06T20:13:41 chembl_compound-pubchem_compound
+> 2024-12-16T01:36:20 chembl_compound-pubchem_compound
Rule for TSV (output/tsv/chembl_compound-pubchem_compound.tsv)
------------------------------
Investigating output/tsv/chembl_compound-pubchem_compound.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:41 +0900
+timestamp: 2024-12-16 01:36:20 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-pubchem_substance if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928334524929328 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:41 chembl_compound-pubchem_substance
+< 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
-> 2024-12-06T20:13:42 chembl_compound-pubchem_substance
+> 2024-12-16T01:36:22 chembl_compound-pubchem_substance
Rule for TSV (output/tsv/chembl_compound-pubchem_substance.tsv)
------------------------------
Investigating output/tsv/chembl_compound-pubchem_substance.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:42 +0900
+timestamp: 2024-12-16 01:36:22 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_compound-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928313558065521 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:42 chembl_compound-pubmed
+< 2024-12-16T01:36:22 chembl_compound-pubmed
togoid-config config/chembl_compound-pubmed update
# Success: output/tsv/chembl_compound-pubmed.tsv is updated
-> 2024-12-06T20:13:45 chembl_compound-pubmed
+> 2024-12-16T01:36:26 chembl_compound-pubmed
Rule for TSV (output/tsv/chembl_compound-pubmed.tsv)
------------------------------
Investigating output/tsv/chembl_compound-pubmed.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:45 +0900
+timestamp: 2024-12-16 01:36:26 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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
-< 2024-12-06T20:13:45 chembl_target-ensembl_gene
+< 2024-12-16T01:36:26 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
-> 2024-12-06T20:13:45 chembl_target-ensembl_gene
+> 2024-12-16T01:36:26 chembl_target-ensembl_gene
Rule for TSV (output/tsv/chembl_target-ensembl_gene.tsv)
------------------------------
Investigating output/tsv/chembl_target-ensembl_gene.tsv
@@ -801,294 +812,294 @@ task needed: true
timestamp: 2023-08-25 17:59:01 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928342236483287 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:45 chembl_target-go
+< 2024-12-16T01:36:26 chembl_target-go
togoid-config config/chembl_target-go update
# Success: output/tsv/chembl_target-go.tsv is updated
-> 2024-12-06T20:13:46 chembl_target-go
+> 2024-12-16T01:36:26 chembl_target-go
Rule for TSV (output/tsv/chembl_target-go.tsv)
------------------------------
Investigating output/tsv/chembl_target-go.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:46 +0900
+timestamp: 2024-12-16 01:36:26 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928342184051828 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:46 chembl_target-interpro
+< 2024-12-16T01:36:26 chembl_target-interpro
togoid-config config/chembl_target-interpro update
# Success: output/tsv/chembl_target-interpro.tsv is updated
-> 2024-12-06T20:13:46 chembl_target-interpro
+> 2024-12-16T01:36:27 chembl_target-interpro
Rule for TSV (output/tsv/chembl_target-interpro.tsv)
------------------------------
Investigating output/tsv/chembl_target-interpro.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:46 +0900
+timestamp: 2024-12-16 01:36:27 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928342523902569 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:46 chembl_target-pdb
+< 2024-12-16T01:36:27 chembl_target-pdb
togoid-config config/chembl_target-pdb update
# Success: output/tsv/chembl_target-pdb.tsv is updated
-> 2024-12-06T20:13:47 chembl_target-pdb
+> 2024-12-16T01:36:27 chembl_target-pdb
Rule for TSV (output/tsv/chembl_target-pdb.tsv)
------------------------------
Investigating output/tsv/chembl_target-pdb.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:47 +0900
+timestamp: 2024-12-16 01:36:27 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928343471057373 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:47 chembl_target-pfam
+< 2024-12-16T01:36:27 chembl_target-pfam
togoid-config config/chembl_target-pfam update
# Success: output/tsv/chembl_target-pfam.tsv is updated
-> 2024-12-06T20:13:47 chembl_target-pfam
+> 2024-12-16T01:36:28 chembl_target-pfam
Rule for TSV (output/tsv/chembl_target-pfam.tsv)
------------------------------
Investigating output/tsv/chembl_target-pfam.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:47 +0900
+timestamp: 2024-12-16 01:36:28 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928344321489318 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:47 chembl_target-reactome_pathway
+< 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
-> 2024-12-06T20:13:48 chembl_target-reactome_pathway
+> 2024-12-16T01:36:28 chembl_target-reactome_pathway
Rule for TSV (output/tsv/chembl_target-reactome_pathway.tsv)
------------------------------
Investigating output/tsv/chembl_target-reactome_pathway.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:48 +0900
+timestamp: 2024-12-16 01:36:28 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for chembl_target-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.92834396043191 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:13:48 chembl_target-uniprot
+< 2024-12-16T01:36:28 chembl_target-uniprot
togoid-config config/chembl_target-uniprot update
# Success: output/tsv/chembl_target-uniprot.tsv is updated
-> 2024-12-06T20:13:48 chembl_target-uniprot
+> 2024-12-16T01:36:29 chembl_target-uniprot
Rule for TSV (output/tsv/chembl_target-uniprot.tsv)
------------------------------
Investigating output/tsv/chembl_target-uniprot.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:13:48 +0900
+timestamp: 2024-12-16 01:36:29 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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
-< 2024-12-06T20:13:48 clinvar-dbsnp
+< 2024-12-16T01:36:29 clinvar-dbsnp
togoid-config config/clinvar-dbsnp update
# Success: output/tsv/clinvar-dbsnp.tsv is updated
-> 2024-12-06T20:14:25 clinvar-dbsnp
+> 2024-12-16T01:37:10 clinvar-dbsnp
Rule for TSV (output/tsv/clinvar-dbsnp.tsv)
------------------------------
Investigating output/tsv/clinvar-dbsnp.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:14:25 +0900
+timestamp: 2024-12-16 01:37:10 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:14:25 +0900)
-latest-prerequisite time: 2024-12-06 20:14:25 +0900
+--prepare:clinvar (2024-12-16 01:37:10 +0900)
+latest-prerequisite time: 2024-12-16 01:37:10 +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
-< 2024-12-06T20:14:25 clinvar-hgnc
+< 2024-12-16T01:37:10 clinvar-hgnc
togoid-config config/clinvar-hgnc update
# Success: output/tsv/clinvar-hgnc.tsv is updated
-> 2024-12-06T20:15:18 clinvar-hgnc
+> 2024-12-16T01:38:03 clinvar-hgnc
Rule for TSV (output/tsv/clinvar-hgnc.tsv)
------------------------------
Investigating output/tsv/clinvar-hgnc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:15:18 +0900
+timestamp: 2024-12-16 01:38:03 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:15:18 +0900)
-latest-prerequisite time: 2024-12-06 20:15:18 +0900
+--prepare:clinvar (2024-12-16 01:38:03 +0900)
+latest-prerequisite time: 2024-12-16 01:38:03 +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
-< 2024-12-06T20:15:18 clinvar-medgen
+< 2024-12-16T01:38:03 clinvar-medgen
togoid-config config/clinvar-medgen update
# Success: output/tsv/clinvar-medgen.tsv is updated
-> 2024-12-06T20:16:55 clinvar-medgen
+> 2024-12-16T01:39:39 clinvar-medgen
Rule for TSV (output/tsv/clinvar-medgen.tsv)
------------------------------
Investigating output/tsv/clinvar-medgen.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:16:55 +0900
+timestamp: 2024-12-16 01:39:39 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:16:55 +0900)
-latest-prerequisite time: 2024-12-06 20:16:55 +0900
+--prepare:clinvar (2024-12-16 01:39:39 +0900)
+latest-prerequisite time: 2024-12-16 01:39:39 +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
-< 2024-12-06T20:16:55 clinvar-mondo
+< 2024-12-16T01:39:39 clinvar-mondo
togoid-config config/clinvar-mondo update
# Success: output/tsv/clinvar-mondo.tsv is updated
-> 2024-12-06T20:18:25 clinvar-mondo
+> 2024-12-16T01:41:09 clinvar-mondo
Rule for TSV (output/tsv/clinvar-mondo.tsv)
------------------------------
Investigating output/tsv/clinvar-mondo.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:18:25 +0900
+timestamp: 2024-12-16 01:41:09 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:18:25 +0900)
-latest-prerequisite time: 2024-12-06 20:18:25 +0900
+--prepare:clinvar (2024-12-16 01:41:09 +0900)
+latest-prerequisite time: 2024-12-16 01:41:09 +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
-< 2024-12-06T20:18:25 clinvar-ncbigene
+< 2024-12-16T01:41:09 clinvar-ncbigene
togoid-config config/clinvar-ncbigene update
# Success: output/tsv/clinvar-ncbigene.tsv is updated
-> 2024-12-06T20:19:17 clinvar-ncbigene
+> 2024-12-16T01:42:01 clinvar-ncbigene
Rule for TSV (output/tsv/clinvar-ncbigene.tsv)
------------------------------
Investigating output/tsv/clinvar-ncbigene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:19:17 +0900
+timestamp: 2024-12-16 01:42:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:19:17 +0900)
-latest-prerequisite time: 2024-12-06 20:19:17 +0900
+--prepare:clinvar (2024-12-16 01:42:01 +0900)
+latest-prerequisite time: 2024-12-16 01:42:01 +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
-< 2024-12-06T20:19:17 clinvar-omim_phenotype
+< 2024-12-16T01:42:01 clinvar-omim_phenotype
togoid-config config/clinvar-omim_phenotype update
# Success: output/tsv/clinvar-omim_phenotype.tsv is updated
-> 2024-12-06T20:20:47 clinvar-omim_phenotype
+> 2024-12-16T01:43:31 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: 2024-12-06 20:20:47 +0900
+timestamp: 2024-12-16 01:43:31 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:20:47 +0900)
-latest-prerequisite time: 2024-12-06 20:20:47 +0900
+--prepare:clinvar (2024-12-16 01:43:31 +0900)
+latest-prerequisite time: 2024-12-16 01:43:31 +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
-< 2024-12-06T20:20:47 clinvar-orphanet_phenotype
+< 2024-12-16T01:43:31 clinvar-orphanet_phenotype
togoid-config config/clinvar-orphanet_phenotype update
# Success: output/tsv/clinvar-orphanet_phenotype.tsv is updated
-> 2024-12-06T20:22:20 clinvar-orphanet_phenotype
+> 2024-12-16T01:45:01 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: 2024-12-06 20:22:20 +0900
+timestamp: 2024-12-16 01:45:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:22:20 +0900)
-latest-prerequisite time: 2024-12-06 20:22:20 +0900
+--prepare:clinvar (2024-12-16 01:45:01 +0900)
+latest-prerequisite time: 2024-12-16 01:45:01 +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
-< 2024-12-06T20:22:20 clinvar-uniprot
+< 2024-12-16T01:45:01 clinvar-uniprot
togoid-config config/clinvar-uniprot update
# Success: output/tsv/clinvar-uniprot.tsv is updated
-> 2024-12-06T20:23:11 clinvar-uniprot
+> 2024-12-16T01:45:51 clinvar-uniprot
Rule for TSV (output/tsv/clinvar-uniprot.tsv)
------------------------------
Investigating output/tsv/clinvar-uniprot.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:23:11 +0900
+timestamp: 2024-12-16 01:45:51 +0900
pre-requisites:
--output/tsv/ ()
---prepare:clinvar (2024-12-06 20:23:11 +0900)
-latest-prerequisite time: 2024-12-06 20:23:11 +0900
+--prepare:clinvar (2024-12-16 01:45:51 +0900)
+latest-prerequisite time: 2024-12-16 01:45:51 +0900
................................
### Update TSV for cog-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -1103,8 +1114,8 @@ task needed: true
timestamp: 2023-07-28 17:55:29 +0900
pre-requisites:
--output/tsv/ ()
---prepare:cog (2024-12-06 20:23:11 +0900)
-latest-prerequisite time: 2024-12-06 20:23:11 +0900
+--prepare:cog (2024-12-16 01:45:51 +0900)
+latest-prerequisite time: 2024-12-16 01:45:51 +0900
................................
### Update TSV for cog-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -1119,103 +1130,105 @@ task needed: true
timestamp: 2023-07-28 17:55:40 +0900
pre-requisites:
--output/tsv/ ()
---prepare:cog (2024-12-06 20:23:11 +0900)
-latest-prerequisite time: 2024-12-06 20:23:11 +0900
+--prepare:cog (2024-12-16 01:45:51 +0900)
+latest-prerequisite time: 2024-12-16 01:45:51 +0900
................................
### Update TSV for doid-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928375202679884 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:23:11 doid-mesh
+< 2024-12-16T01:45:51 doid-mesh
togoid-config config/doid-mesh update
# Success: output/tsv/doid-mesh.tsv is updated
-> 2024-12-06T20:23:11 doid-mesh
+> 2024-12-16T01:45:52 doid-mesh
Rule for TSV (output/tsv/doid-mesh.tsv)
------------------------------
Investigating output/tsv/doid-mesh.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:23:11 +0900
+timestamp: 2024-12-16 01:45:52 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for doid-ncit_disease if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928375909455555 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:23:11 doid-ncit_disease
+< 2024-12-16T01:45:52 doid-ncit_disease
togoid-config config/doid-ncit_disease update
# Success: output/tsv/doid-ncit_disease.tsv is updated
-> 2024-12-06T20:23:12 doid-ncit_disease
+> 2024-12-16T01:45:52 doid-ncit_disease
Rule for TSV (output/tsv/doid-ncit_disease.tsv)
------------------------------
Investigating output/tsv/doid-ncit_disease.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:23:12 +0900
+timestamp: 2024-12-16 01:45:52 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for doid-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928375983137593 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:23:12 doid-omim_phenotype
+< 2024-12-16T01:45:52 doid-omim_phenotype
togoid-config config/doid-omim_phenotype update
# Success: output/tsv/doid-omim_phenotype.tsv is updated
-> 2024-12-06T20:23:12 doid-omim_phenotype
+> 2024-12-16T01:45:53 doid-omim_phenotype
Rule for TSV (output/tsv/doid-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/doid-omim_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:23:12 +0900
+timestamp: 2024-12-16 01:45:53 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for ensembl_gene-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.927711888958901 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:23:12 ensembl_gene-affy_probeset
+< 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
-> 2024-12-06T20:24:01 ensembl_gene-affy_probeset
+> 2024-12-16T01:46:57 ensembl_gene-affy_probeset
Rule for TSV (output/tsv/ensembl_gene-affy_probeset.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-affy_probeset.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:24:01 +0900
+timestamp: 2024-12-16 01:46:57 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:24:01 +0900)
-latest-prerequisite time: 2024-12-06 20:24:01 +0900
+--prepare:ensembl (2024-12-16 01:46:57 +0900)
+latest-prerequisite time: 2024-12-16 01:46:57 +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 6.9270129728564696 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_gene-ensembl_protein.tsv is created 9.22300119364082 days ago (will be updated when >5 days)
## Update config/ensembl_gene-ensembl_protein/config.yaml => output/tsv/ensembl_gene-ensembl_protein.tsv
-< 2024-12-06T20:24:01 ensembl_gene-ensembl_protein
+< 2024-12-16T01:46:57 ensembl_gene-ensembl_protein
togoid-config config/ensembl_gene-ensembl_protein update
-# Success: output/tsv/ensembl_gene-ensembl_protein.tsv is updated
-> 2024-12-06T20:25:50 ensembl_gene-ensembl_protein
+# 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
Rule for TSV (output/tsv/ensembl_gene-ensembl_protein.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-ensembl_protein.tsv
@@ -1224,19 +1237,21 @@ task needed: true
timestamp: 2024-12-06 20:25:50 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:25:50 +0900)
-latest-prerequisite time: 2024-12-06 20:25:50 +0900
+--prepare:ensembl (2024-12-16 01:46:57 +0900)
+latest-prerequisite time: 2024-12-16 01:46:57 +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 6.926867080370209 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_gene-ensembl_transcript.tsv is created 9.221533021723934 days ago (will be updated when >5 days)
## Update config/ensembl_gene-ensembl_transcript/config.yaml => output/tsv/ensembl_gene-ensembl_transcript.tsv
-< 2024-12-06T20:25:50 ensembl_gene-ensembl_transcript
+< 2024-12-16T01:46:57 ensembl_gene-ensembl_transcript
togoid-config config/ensembl_gene-ensembl_transcript update
-# Success: output/tsv/ensembl_gene-ensembl_transcript.tsv is updated
-> 2024-12-06T20:27:57 ensembl_gene-ensembl_transcript
+# 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
Rule for TSV (output/tsv/ensembl_gene-ensembl_transcript.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-ensembl_transcript.tsv
@@ -1245,103 +1260,42 @@ task needed: true
timestamp: 2024-12-06 20:27:57 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:27:57 +0900)
-latest-prerequisite time: 2024-12-06 20:27:57 +0900
+--prepare:ensembl (2024-12-16 01:46:57 +0900)
+latest-prerequisite time: 2024-12-16 01:46:57 +0900
................................
### Update TSV for ensembl_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928332335791401 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:27:57 ensembl_gene-hgnc
+< 2024-12-16T01:46:57 ensembl_gene-hgnc
togoid-config config/ensembl_gene-hgnc update
# Success: output/tsv/ensembl_gene-hgnc.tsv is updated
-> 2024-12-06T20:27:57 ensembl_gene-hgnc
+> 2024-12-16T01:46:58 ensembl_gene-hgnc
Rule for TSV (output/tsv/ensembl_gene-hgnc.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-hgnc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:27:57 +0900
+timestamp: 2024-12-16 01:46:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:27:57 +0900)
-latest-prerequisite time: 2024-12-06 20:27:57 +0900
+--prepare:ensembl (2024-12-16 01:46:58 +0900)
+latest-prerequisite time: 2024-12-16 01:46:58 +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 6.92697722170368 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_gene-ncbigene.tsv is created 9.220169899221956 days ago (will be updated when >5 days)
## Update config/ensembl_gene-ncbigene/config.yaml => output/tsv/ensembl_gene-ncbigene.tsv
-< 2024-12-06T20:27:57 ensembl_gene-ncbigene
+< 2024-12-16T01:46:58 ensembl_gene-ncbigene
togoid-config config/ensembl_gene-ncbigene update
-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
-> 2024-12-06T20:29:55 ensembl_gene-ncbigene
+# 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
Rule for TSV (output/tsv/ensembl_gene-ncbigene.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-ncbigene.tsv
@@ -1350,75 +1304,21 @@ task needed: true
timestamp: 2024-12-06 20:29:55 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:29:55 +0900)
-latest-prerequisite time: 2024-12-06 20:29:55 +0900
+--prepare:ensembl (2024-12-16 01:46:58 +0900)
+latest-prerequisite time: 2024-12-16 01:46:58 +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 6.927381543930127 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_gene-uniprot.tsv is created 9.219176207811111 days ago (will be updated when >5 days)
## Update config/ensembl_gene-uniprot/config.yaml => output/tsv/ensembl_gene-uniprot.tsv
-< 2024-12-06T20:29:55 ensembl_gene-uniprot
+< 2024-12-16T01:46:58 ensembl_gene-uniprot
togoid-config config/ensembl_gene-uniprot update
-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
-> 2024-12-06T20:31:21 ensembl_gene-uniprot
+# 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
Rule for TSV (output/tsv/ensembl_gene-uniprot.tsv)
------------------------------
Investigating output/tsv/ensembl_gene-uniprot.tsv
@@ -1427,19 +1327,21 @@ task needed: true
timestamp: 2024-12-06 20:31:21 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:31:21 +0900)
-latest-prerequisite time: 2024-12-06 20:31:21 +0900
+--prepare:ensembl (2024-12-16 01:46:58 +0900)
+latest-prerequisite time: 2024-12-16 01:46:58 +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 6.927031905648391 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_protein-ensembl_transcript.tsv is created 9.217785663917546 days ago (will be updated when >5 days)
## Update config/ensembl_protein-ensembl_transcript/config.yaml => output/tsv/ensembl_protein-ensembl_transcript.tsv
-< 2024-12-06T20:31:21 ensembl_protein-ensembl_transcript
+< 2024-12-16T01:46:58 ensembl_protein-ensembl_transcript
togoid-config config/ensembl_protein-ensembl_transcript update
-# Success: output/tsv/ensembl_protein-ensembl_transcript.tsv is updated
-> 2024-12-06T20:33:22 ensembl_protein-ensembl_transcript
+# 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
Rule for TSV (output/tsv/ensembl_protein-ensembl_transcript.tsv)
------------------------------
Investigating output/tsv/ensembl_protein-ensembl_transcript.tsv
@@ -1448,40 +1350,42 @@ task needed: true
timestamp: 2024-12-06 20:33:22 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:33:22 +0900)
-latest-prerequisite time: 2024-12-06 20:33:22 +0900
+--prepare:ensembl (2024-12-16 01:46:59 +0900)
+latest-prerequisite time: 2024-12-16 01:46:59 +0900
................................
### Update TSV for ensembl_transcript-affy_probeset if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.927743116410301 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:33:22 ensembl_transcript-affy_probeset
+< 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
-> 2024-12-06T20:34:15 ensembl_transcript-affy_probeset
+> 2024-12-16T01:48:04 ensembl_transcript-affy_probeset
Rule for TSV (output/tsv/ensembl_transcript-affy_probeset.tsv)
------------------------------
Investigating output/tsv/ensembl_transcript-affy_probeset.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:34:15 +0900
+timestamp: 2024-12-16 01:48:04 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:34:15 +0900)
-latest-prerequisite time: 2024-12-06 20:34:15 +0900
+--prepare:ensembl (2024-12-16 01:48:04 +0900)
+latest-prerequisite time: 2024-12-16 01:48:04 +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 6.925461128889387 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_transcript-go.tsv is created 9.21511766733595 days ago (will be updated when >5 days)
## Update config/ensembl_transcript-go/config.yaml => output/tsv/ensembl_transcript-go.tsv
-< 2024-12-06T20:34:15 ensembl_transcript-go
+< 2024-12-16T01:48:04 ensembl_transcript-go
togoid-config config/ensembl_transcript-go update
-# Success: output/tsv/ensembl_transcript-go.tsv is updated
-> 2024-12-06T20:38:18 ensembl_transcript-go
+# 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
Rule for TSV (output/tsv/ensembl_transcript-go.tsv)
------------------------------
Investigating output/tsv/ensembl_transcript-go.tsv
@@ -1490,108 +1394,42 @@ task needed: true
timestamp: 2024-12-06 20:38:18 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:38:18 +0900)
-latest-prerequisite time: 2024-12-06 20:38:18 +0900
+--prepare:ensembl (2024-12-16 01:48:04 +0900)
+latest-prerequisite time: 2024-12-16 01:48:04 +0900
................................
### Update TSV for ensembl_transcript-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928266259554166 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:38:18 ensembl_transcript-hgnc
+< 2024-12-16T01:48:04 ensembl_transcript-hgnc
togoid-config config/ensembl_transcript-hgnc update
# Success: output/tsv/ensembl_transcript-hgnc.tsv is updated
-> 2024-12-06T20:38:19 ensembl_transcript-hgnc
+> 2024-12-16T01:48:05 ensembl_transcript-hgnc
Rule for TSV (output/tsv/ensembl_transcript-hgnc.tsv)
------------------------------
Investigating output/tsv/ensembl_transcript-hgnc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:38:19 +0900
+timestamp: 2024-12-16 01:48:05 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:38:19 +0900)
-latest-prerequisite time: 2024-12-06 20:38:19 +0900
+--prepare:ensembl (2024-12-16 01:48:05 +0900)
+latest-prerequisite time: 2024-12-16 01:48:05 +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 6.9258990269107406 days ago (will be updated when >5 days)
+# File output/tsv/ensembl_transcript-refseq_rna.tsv is created 9.212762598192556 days ago (will be updated when >5 days)
## Update config/ensembl_transcript-refseq_rna/config.yaml => output/tsv/ensembl_transcript-refseq_rna.tsv
-< 2024-12-06T20:38:19 ensembl_transcript-refseq_rna
+< 2024-12-16T01:48:05 ensembl_transcript-refseq_rna
togoid-config config/ensembl_transcript-refseq_rna update
-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
-> 2024-12-06T20:41:42 ensembl_transcript-refseq_rna
+# 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
Rule for TSV (output/tsv/ensembl_transcript-refseq_rna.tsv)
------------------------------
Investigating output/tsv/ensembl_transcript-refseq_rna.tsv
@@ -1600,64 +1438,70 @@ task needed: true
timestamp: 2024-12-06 20:41:42 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ensembl (2024-12-06 20:41:42 +0900)
-latest-prerequisite time: 2024-12-06 20:41:42 +0900
+--prepare:ensembl (2024-12-16 01:48:05 +0900)
+latest-prerequisite time: 2024-12-16 01:48:05 +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 6.928251772042697 days ago (will be updated when >5 days)
+# File output/tsv/gea-bioproject.tsv is created 9.212761025845255 days ago (will be updated when >5 days)
## Update config/gea-bioproject/config.yaml => output/tsv/gea-bioproject.tsv
-< 2024-12-06T20:41:42 gea-bioproject
+< 2024-12-16T01:48:05 gea-bioproject
togoid-config config/gea-bioproject update
-# Success: output/tsv/gea-bioproject.tsv is updated
-> 2024-12-06T20:41:43 gea-bioproject
+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
Rule for TSV (output/tsv/gea-bioproject.tsv)
------------------------------
Investigating output/tsv/gea-bioproject.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:41:43 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.928251367233993 days ago (will be updated when >5 days)
+# File output/tsv/gea-biosample.tsv is created 9.214230862464653 days ago (will be updated when >5 days)
## Update config/gea-biosample/config.yaml => output/tsv/gea-biosample.tsv
-< 2024-12-06T20:41:43 gea-biosample
+< 2024-12-16T01:50:13 gea-biosample
togoid-config config/gea-biosample update
-# Success: output/tsv/gea-biosample.tsv is updated
-> 2024-12-06T20:41:43 gea-biosample
+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
Rule for TSV (output/tsv/gea-biosample.tsv)
------------------------------
Investigating output/tsv/gea-biosample.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:41:43 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 111.968401502289 days ago (will be updated when >5 days)
+# File output/tsv/glycomotif-glytoucan.tsv is created 121.18410769166488 days ago (will be updated when >5 days)
## Update config/glycomotif-glytoucan/config.yaml => output/tsv/glycomotif-glytoucan.tsv
-< 2024-12-06T20:41:43 glycomotif-glytoucan
+< 2024-12-16T01:52:20 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
-> 2024-12-06T20:42:15 glycomotif-glytoucan
+> 2024-12-16T01:52:52 glycomotif-glytoucan
Rule for TSV (output/tsv/glycomotif-glytoucan.tsv)
------------------------------
Investigating output/tsv/glycomotif-glytoucan.tsv
@@ -1666,19 +1510,20 @@ task needed: true
timestamp: 2024-08-16 21:27:13 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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
-< 2024-12-06T20:42:15 glytoucan-doid
+< 2024-12-16T01:52:52 glytoucan-doid
togoid-config config/glytoucan-doid update
-# Error: output/tsv/glytoucan-doid.tsv new file size per old 1538 / 4376 = 0.35146252285191953 < 0.5
+# 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
-> 2024-12-06T20:42:22 glytoucan-doid
+> 2024-12-16T01:52:56 glytoucan-doid
Rule for TSV (output/tsv/glytoucan-doid.tsv)
------------------------------
Investigating output/tsv/glytoucan-doid.tsv
@@ -1687,58 +1532,58 @@ task needed: true
timestamp: 2024-03-22 20:42:15 +0900
pre-requisites:
--output/tsv/ ()
---prepare:glytoucan (2024-12-06 20:42:22 +0900)
-latest-prerequisite time: 2024-12-06 20:42:22 +0900
+--prepare:glytoucan (2024-12-16 01:52:56 +0900)
+latest-prerequisite time: 2024-12-16 01:52:56 +0900
................................
### Update TSV for glytoucan-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:22 glytoucan-ncbigene
+< 2024-12-16T01:52:56 glytoucan-ncbigene
togoid-config config/glytoucan-ncbigene update
# Success: output/tsv/glytoucan-ncbigene.tsv is updated
-> 2024-12-06T20:42:23 glytoucan-ncbigene
+> 2024-12-16T01:52:57 glytoucan-ncbigene
Rule for TSV (output/tsv/glytoucan-ncbigene.tsv)
------------------------------
Investigating output/tsv/glytoucan-ncbigene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:23 +0900
+timestamp: 2024-12-16 01:52:57 +0900
pre-requisites:
--output/tsv/ ()
---prepare:glytoucan (2024-12-06 20:42:23 +0900)
-latest-prerequisite time: 2024-12-06 20:42:23 +0900
+--prepare:glytoucan (2024-12-16 01:52:57 +0900)
+latest-prerequisite time: 2024-12-16 01:52:57 +0900
................................
### Update TSV for glytoucan-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:23 glytoucan-uniprot
+< 2024-12-16T01:52:57 glytoucan-uniprot
togoid-config config/glytoucan-uniprot update
# Success: output/tsv/glytoucan-uniprot.tsv is updated
-> 2024-12-06T20:42:25 glytoucan-uniprot
+> 2024-12-16T01:52:59 glytoucan-uniprot
Rule for TSV (output/tsv/glytoucan-uniprot.tsv)
------------------------------
Investigating output/tsv/glytoucan-uniprot.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:25 +0900
+timestamp: 2024-12-16 01:52:59 +0900
pre-requisites:
--output/tsv/ ()
---prepare:glytoucan (2024-12-06 20:42:25 +0900)
-latest-prerequisite time: 2024-12-06 20:42:25 +0900
+--prepare:glytoucan (2024-12-16 01:52:59 +0900)
+latest-prerequisite time: 2024-12-16 01:52:59 +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
-< 2024-12-06T20:42:25 hgnc-ccds
+< 2024-12-16T01:52:59 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
-> 2024-12-06T20:42:26 hgnc-ccds
+> 2024-12-16T01:52:59 hgnc-ccds
Rule for TSV (output/tsv/hgnc-ccds.tsv)
------------------------------
Investigating output/tsv/hgnc-ccds.tsv
@@ -1747,288 +1592,287 @@ task needed: true
timestamp: 2024-08-16 21:27:23 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:26 +0900)
-latest-prerequisite time: 2024-12-06 20:42:26 +0900
+--prepare:hgnc (2024-12-16 01:52:59 +0900)
+latest-prerequisite time: 2024-12-16 01:52:59 +0900
................................
### Update TSV for hgnc-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:26 hgnc-ec
+< 2024-12-16T01:52:59 hgnc-ec
togoid-config config/hgnc-ec update
# Success: output/tsv/hgnc-ec.tsv is updated
-> 2024-12-06T20:42:26 hgnc-ec
+> 2024-12-16T01:53:00 hgnc-ec
Rule for TSV (output/tsv/hgnc-ec.tsv)
------------------------------
Investigating output/tsv/hgnc-ec.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:26 +0900
+timestamp: 2024-12-16 01:53:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:26 +0900)
-latest-prerequisite time: 2024-12-06 20:42:26 +0900
+--prepare:hgnc (2024-12-16 01:53:00 +0900)
+latest-prerequisite time: 2024-12-16 01:53:00 +0900
................................
### Update TSV for hgnc-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:26 hgnc-ensembl_gene
+< 2024-12-16T01:53:00 hgnc-ensembl_gene
togoid-config config/hgnc-ensembl_gene update
# Success: output/tsv/hgnc-ensembl_gene.tsv is updated
-> 2024-12-06T20:42:27 hgnc-ensembl_gene
+> 2024-12-16T01:53:00 hgnc-ensembl_gene
Rule for TSV (output/tsv/hgnc-ensembl_gene.tsv)
------------------------------
Investigating output/tsv/hgnc-ensembl_gene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:27 +0900
+timestamp: 2024-12-16 01:53:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:27 +0900)
-latest-prerequisite time: 2024-12-06 20:42:27 +0900
+--prepare:hgnc (2024-12-16 01:53:00 +0900)
+latest-prerequisite time: 2024-12-16 01:53:00 +0900
................................
### Update TSV for hgnc-hgnc_symbol if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:27 hgnc-hgnc_symbol
+< 2024-12-16T01:53:00 hgnc-hgnc_symbol
togoid-config config/hgnc-hgnc_symbol update
# Success: output/tsv/hgnc-hgnc_symbol.tsv is updated
-> 2024-12-06T20:42:27 hgnc-hgnc_symbol
+> 2024-12-16T01:53:01 hgnc-hgnc_symbol
Rule for TSV (output/tsv/hgnc-hgnc_symbol.tsv)
------------------------------
Investigating output/tsv/hgnc-hgnc_symbol.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:27 +0900
+timestamp: 2024-12-16 01:53:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:27 +0900)
-latest-prerequisite time: 2024-12-06 20:42:27 +0900
+--prepare:hgnc (2024-12-16 01:53:01 +0900)
+latest-prerequisite time: 2024-12-16 01:53:01 +0900
................................
### Update TSV for hgnc-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:27 hgnc-insdc
+< 2024-12-16T01:53:01 hgnc-insdc
togoid-config config/hgnc-insdc update
# Success: output/tsv/hgnc-insdc.tsv is updated
-> 2024-12-06T20:42:27 hgnc-insdc
+> 2024-12-16T01:53:01 hgnc-insdc
Rule for TSV (output/tsv/hgnc-insdc.tsv)
------------------------------
Investigating output/tsv/hgnc-insdc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:27 +0900
+timestamp: 2024-12-16 01:53:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:27 +0900)
-latest-prerequisite time: 2024-12-06 20:42:27 +0900
+--prepare:hgnc (2024-12-16 01:53:01 +0900)
+latest-prerequisite time: 2024-12-16 01:53:01 +0900
................................
### Update TSV for hgnc-lrg if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:27 hgnc-lrg
+< 2024-12-16T01:53:01 hgnc-lrg
togoid-config config/hgnc-lrg update
# Success: output/tsv/hgnc-lrg.tsv is updated
-> 2024-12-06T20:42:28 hgnc-lrg
+> 2024-12-16T01:53:02 hgnc-lrg
Rule for TSV (output/tsv/hgnc-lrg.tsv)
------------------------------
Investigating output/tsv/hgnc-lrg.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:28 +0900
+timestamp: 2024-12-16 01:53:02 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:28 +0900)
-latest-prerequisite time: 2024-12-06 20:42:28 +0900
+--prepare:hgnc (2024-12-16 01:53:02 +0900)
+latest-prerequisite time: 2024-12-16 01:53:02 +0900
................................
### Update TSV for hgnc-mgi_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:28 hgnc-mgi_gene
+< 2024-12-16T01:53:02 hgnc-mgi_gene
togoid-config config/hgnc-mgi_gene update
# Success: output/tsv/hgnc-mgi_gene.tsv is updated
-> 2024-12-06T20:42:28 hgnc-mgi_gene
+> 2024-12-16T01:53:02 hgnc-mgi_gene
Rule for TSV (output/tsv/hgnc-mgi_gene.tsv)
------------------------------
Investigating output/tsv/hgnc-mgi_gene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:28 +0900
+timestamp: 2024-12-16 01:53:02 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:28 +0900)
-latest-prerequisite time: 2024-12-06 20:42:28 +0900
+--prepare:hgnc (2024-12-16 01:53:02 +0900)
+latest-prerequisite time: 2024-12-16 01:53:02 +0900
................................
### Update TSV for hgnc-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:28 hgnc-mirbase
+< 2024-12-16T01:53:02 hgnc-mirbase
togoid-config config/hgnc-mirbase update
# Success: output/tsv/hgnc-mirbase.tsv is updated
-> 2024-12-06T20:42:29 hgnc-mirbase
+> 2024-12-16T01:53:03 hgnc-mirbase
Rule for TSV (output/tsv/hgnc-mirbase.tsv)
------------------------------
Investigating output/tsv/hgnc-mirbase.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:29 +0900
+timestamp: 2024-12-16 01:53:03 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:29 +0900)
-latest-prerequisite time: 2024-12-06 20:42:29 +0900
+--prepare:hgnc (2024-12-16 01:53:03 +0900)
+latest-prerequisite time: 2024-12-16 01:53:03 +0900
................................
### Update TSV for hgnc-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:29 hgnc-ncbigene
+< 2024-12-16T01:53:03 hgnc-ncbigene
togoid-config config/hgnc-ncbigene update
# Success: output/tsv/hgnc-ncbigene.tsv is updated
-> 2024-12-06T20:42:30 hgnc-ncbigene
+> 2024-12-16T01:53:03 hgnc-ncbigene
Rule for TSV (output/tsv/hgnc-ncbigene.tsv)
------------------------------
Investigating output/tsv/hgnc-ncbigene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:30 +0900
+timestamp: 2024-12-16 01:53:03 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:30 +0900)
-latest-prerequisite time: 2024-12-06 20:42:30 +0900
+--prepare:hgnc (2024-12-16 01:53:03 +0900)
+latest-prerequisite time: 2024-12-16 01:53:03 +0900
................................
### Update TSV for hgnc-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:30 hgnc-omim_gene
+< 2024-12-16T01:53:03 hgnc-omim_gene
togoid-config config/hgnc-omim_gene update
# Success: output/tsv/hgnc-omim_gene.tsv is updated
-> 2024-12-06T20:42:30 hgnc-omim_gene
+> 2024-12-16T01:53:04 hgnc-omim_gene
Rule for TSV (output/tsv/hgnc-omim_gene.tsv)
------------------------------
Investigating output/tsv/hgnc-omim_gene.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:30 +0900
+timestamp: 2024-12-16 01:53:04 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:30 +0900)
-latest-prerequisite time: 2024-12-06 20:42:30 +0900
+--prepare:hgnc (2024-12-16 01:53:04 +0900)
+latest-prerequisite time: 2024-12-16 01:53:04 +0900
................................
### Update TSV for hgnc-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:30 hgnc-pubmed
+< 2024-12-16T01:53:04 hgnc-pubmed
togoid-config config/hgnc-pubmed update
# Success: output/tsv/hgnc-pubmed.tsv is updated
-> 2024-12-06T20:42:31 hgnc-pubmed
+> 2024-12-16T01:53:04 hgnc-pubmed
Rule for TSV (output/tsv/hgnc-pubmed.tsv)
------------------------------
Investigating output/tsv/hgnc-pubmed.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:31 +0900
+timestamp: 2024-12-16 01:53:04 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:31 +0900)
-latest-prerequisite time: 2024-12-06 20:42:31 +0900
+--prepare:hgnc (2024-12-16 01:53:04 +0900)
+latest-prerequisite time: 2024-12-16 01:53:04 +0900
................................
### Update TSV for hgnc-refseq_genomic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:31 hgnc-refseq_genomic
+< 2024-12-16T01:53:04 hgnc-refseq_genomic
togoid-config config/hgnc-refseq_genomic update
# Success: output/tsv/hgnc-refseq_genomic.tsv is updated
-> 2024-12-06T20:42:31 hgnc-refseq_genomic
+> 2024-12-16T01:53:05 hgnc-refseq_genomic
Rule for TSV (output/tsv/hgnc-refseq_genomic.tsv)
------------------------------
Investigating output/tsv/hgnc-refseq_genomic.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:31 +0900
+timestamp: 2024-12-16 01:53:05 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:31 +0900)
-latest-prerequisite time: 2024-12-06 20:42:31 +0900
+--prepare:hgnc (2024-12-16 01:53:05 +0900)
+latest-prerequisite time: 2024-12-16 01:53:05 +0900
................................
-### Update TSV for hgnc-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
-# File output/tsv/hgnc-refseq_rna.tsv is newer than config/hgnc-refseq_rna/config.yaml
-# File output/tsv/hgnc-refseq_rna.tsv is older than input/hgnc/download.lock
+### 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
-< 2024-12-06T20:42:31 hgnc-refseq_rna
+< 2024-12-16T01:53:05 hgnc-refseq_rna
togoid-config config/hgnc-refseq_rna update
# Success: output/tsv/hgnc-refseq_rna.tsv is updated
-> 2024-12-06T20:42:32 hgnc-refseq_rna
+rm: remove write-protected regular file ‘output/tsv/hgnc-refseq_rna.tsv.old’? > 2024-12-16T15:21:11 hgnc-refseq_rna
Rule for TSV (output/tsv/hgnc-refseq_rna.tsv)
------------------------------
Investigating output/tsv/hgnc-refseq_rna.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:32 +0900
+timestamp: 2024-12-16 01:53:05 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:32 +0900)
-latest-prerequisite time: 2024-12-06 20:42:32 +0900
+--prepare:hgnc (2024-12-16 15:21:11 +0900)
+latest-prerequisite time: 2024-12-16 15:21:11 +0900
................................
### Update TSV for hgnc-rgd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:32 hgnc-rgd
+< 2024-12-16T15:21:11 hgnc-rgd
togoid-config config/hgnc-rgd update
# Success: output/tsv/hgnc-rgd.tsv is updated
-> 2024-12-06T20:42:32 hgnc-rgd
+> 2024-12-16T15:21:12 hgnc-rgd
Rule for TSV (output/tsv/hgnc-rgd.tsv)
------------------------------
Investigating output/tsv/hgnc-rgd.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:32 +0900
+timestamp: 2024-12-16 15:21:12 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:32 +0900)
-latest-prerequisite time: 2024-12-06 20:42:32 +0900
+--prepare:hgnc (2024-12-16 15:21:12 +0900)
+latest-prerequisite time: 2024-12-16 15:21:12 +0900
................................
### Update TSV for hgnc-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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
-< 2024-12-06T20:42:32 hgnc-uniprot
+< 2024-12-16T15:21:12 hgnc-uniprot
togoid-config config/hgnc-uniprot update
# Success: output/tsv/hgnc-uniprot.tsv is updated
-> 2024-12-06T20:42:33 hgnc-uniprot
+> 2024-12-16T15:21:13 hgnc-uniprot
Rule for TSV (output/tsv/hgnc-uniprot.tsv)
------------------------------
Investigating output/tsv/hgnc-uniprot.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:42:33 +0900
+timestamp: 2024-12-16 15:21:13 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hgnc (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:hgnc (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for hmdb-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2043,8 +1887,8 @@ task needed: true
timestamp: 2023-07-03 13:03:28 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hmdb (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:hmdb (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for hmdb-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2059,8 +1903,8 @@ task needed: true
timestamp: 2023-07-03 13:03:51 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hmdb (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:hmdb (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for hmdb-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2075,8 +1919,8 @@ task needed: true
timestamp: 2024-01-20 02:10:47 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hmdb (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:hmdb (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for hmdb-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2091,8 +1935,8 @@ task needed: true
timestamp: 2023-07-03 13:06:27 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hmdb (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:hmdb (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for homologene-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2107,145 +1951,165 @@ task needed: true
timestamp: 2023-06-02 19:58:16 +0900
pre-requisites:
--output/tsv/ ()
---prepare:homologene (2024-12-06 20:42:33 +0900)
-latest-prerequisite time: 2024-12-06 20:42:33 +0900
+--prepare:homologene (2024-12-16 15:21:13 +0900)
+latest-prerequisite time: 2024-12-16 15:21:13 +0900
................................
### Update TSV for hp_inheritance-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.928181655277801 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:42:33 hp_inheritance-omim_phenotype
+< 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
-> 2024-12-06T20:42:34 hp_inheritance-omim_phenotype
+> 2024-12-16T15:21:14 hp_inheritance-omim_phenotype
Rule for TSV (output/tsv/hp_inheritance-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/hp_inheritance-omim_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:42:34 +0900
+timestamp: 2024-12-16 15:21:14 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
-### Update TSV for hp_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### Update TSV for hp_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 newer than input/hp_phenotype/download.lock
-# => Preserving output/tsv/hp_phenotype-omim_phenotype.tsv
+# 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
Rule for TSV (output/tsv/hp_phenotype-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/hp_phenotype-omim_phenotype.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-08-16 21:27:32 +0900
+timestamp: 2024-12-16 15:21:14 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hp_phenotype (2024-12-06 20:42:34 +0900)
-latest-prerequisite time: 2024-12-06 20:42:34 +0900
+--prepare:hp_phenotype (2024-12-16 15:21:14 +0900)
+latest-prerequisite time: 2024-12-16 15:21:14 +0900
................................
-### Update TSV for hp_phenotype-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### Update TSV for hp_phenotype-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 newer than input/hp_phenotype/download.lock
-# => Preserving output/tsv/hp_phenotype-orphanet_phenotype.tsv
+# 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
Rule for TSV (output/tsv/hp_phenotype-orphanet_phenotype.tsv)
------------------------------
Investigating output/tsv/hp_phenotype-orphanet_phenotype.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-08-16 21:27:33 +0900
+timestamp: 2024-12-16 15:21:15 +0900
pre-requisites:
--output/tsv/ ()
---prepare:hp_phenotype (2024-12-06 20:42:34 +0900)
-latest-prerequisite time: 2024-12-06 20:42:34 +0900
+--prepare:hp_phenotype (2024-12-16 15:21:15 +0900)
+latest-prerequisite time: 2024-12-16 15:21:15 +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 6.927923790339248 days ago (will be updated when >5 days)
+# File output/tsv/insdc-bioproject.tsv is created 9.776600484627188 days ago (will be updated when >5 days)
## Update config/insdc-bioproject/config.yaml => output/tsv/insdc-bioproject.tsv
-< 2024-12-06T20:42:34 insdc-bioproject
+< 2024-12-16T15:21:15 insdc-bioproject
togoid-config config/insdc-bioproject update
-# Success: output/tsv/insdc-bioproject.tsv is updated
-> 2024-12-06T20:42:57 insdc-bioproject
+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
Rule for TSV (output/tsv/insdc-bioproject.tsv)
------------------------------
Investigating output/tsv/insdc-bioproject.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:42:57 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.927321676438819 days ago (will be updated when >5 days)
+# File output/tsv/insdc-biosample.tsv is created 9.77720530920839 days ago (will be updated when >5 days)
## Update config/insdc-biosample/config.yaml => output/tsv/insdc-biosample.tsv
-< 2024-12-06T20:42:57 insdc-biosample
+< 2024-12-16T15:23:23 insdc-biosample
togoid-config config/insdc-biosample update
-# Success: output/tsv/insdc-biosample.tsv is updated
-> 2024-12-06T20:44:12 insdc-biosample
+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
Rule for TSV (output/tsv/insdc-biosample.tsv)
------------------------------
Investigating output/tsv/insdc-biosample.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:44:12 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.928176697863982 days ago (will be updated when >5 days)
+# File output/tsv/insdc_master-bioproject.tsv is created 9.778663057370961 days ago (will be updated when >5 days)
## Update config/insdc_master-bioproject/config.yaml => output/tsv/insdc_master-bioproject.tsv
-< 2024-12-06T20:44:12 insdc_master-bioproject
+< 2024-12-16T15:25:30 insdc_master-bioproject
togoid-config config/insdc_master-bioproject update
-# Success: output/tsv/insdc_master-bioproject.tsv is updated
-> 2024-12-06T20:44:14 insdc_master-bioproject
+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
Rule for TSV (output/tsv/insdc_master-bioproject.tsv)
------------------------------
Investigating output/tsv/insdc_master-bioproject.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:44:14 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.928176776981875 days ago (will be updated when >5 days)
+# File output/tsv/insdc_master-biosample.tsv is created 9.780121934212882 days ago (will be updated when >5 days)
## Update config/insdc_master-biosample/config.yaml => output/tsv/insdc_master-biosample.tsv
-< 2024-12-06T20:44:14 insdc_master-biosample
+< 2024-12-16T15:27:38 insdc_master-biosample
togoid-config config/insdc_master-biosample update
-# Success: output/tsv/insdc_master-biosample.tsv is updated
-> 2024-12-06T20:44:15 insdc_master-biosample
+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
Rule for TSV (output/tsv/insdc_master-biosample.tsv)
------------------------------
Investigating output/tsv/insdc_master-biosample.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:44:15 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for interpro-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2260,8 +2124,8 @@ task needed: true
timestamp: 2024-11-29 22:27:40 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2276,8 +2140,8 @@ task needed: true
timestamp: 2024-11-29 22:27:43 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2292,8 +2156,8 @@ task needed: true
timestamp: 2024-11-29 22:27:44 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-prosite if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2308,8 +2172,8 @@ task needed: true
timestamp: 2024-11-29 22:27:46 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2324,8 +2188,8 @@ task needed: true
timestamp: 2024-11-29 22:27:48 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2340,8 +2204,8 @@ task needed: true
timestamp: 2024-11-29 22:27:50 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-smart if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2356,8 +2220,8 @@ task needed: true
timestamp: 2024-11-29 22:27:51 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +0900
................................
### Update TSV for interpro-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -2372,79 +2236,88 @@ task needed: true
timestamp: 2024-11-30 02:23:51 +0900
pre-requisites:
--output/tsv/ ()
---prepare:interpro (2024-12-06 20:44:15 +0900)
-latest-prerequisite time: 2024-12-06 20:44:15 +0900
+--prepare:interpro (2024-12-16 15:29:45 +0900)
+latest-prerequisite time: 2024-12-16 15:29:45 +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 6.76415322114956 days ago (will be updated when >5 days)
+# File output/tsv/jga_study-jga_dataset.tsv is created 9.78159249394478 days ago (will be updated when >5 days)
## Update config/jga_study-jga_dataset/config.yaml => output/tsv/jga_study-jga_dataset.tsv
-< 2024-12-06T20:44:15 jga_study-jga_dataset
+< 2024-12-16T15:29:45 jga_study-jga_dataset
togoid-config config/jga_study-jga_dataset update
-# Success: output/tsv/jga_study-jga_dataset.tsv is updated
-> 2024-12-06T20:44:16 jga_study-jga_dataset
+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
Rule for TSV (output/tsv/jga_study-jga_dataset.tsv)
------------------------------
Investigating output/tsv/jga_study-jga_dataset.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:44:16 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.764153194402755 days ago (will be updated when >5 days)
+# File output/tsv/jga_study-nbdc_human_db.tsv is created 9.783062965355603 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
-< 2024-12-06T20:44:16 jga_study-nbdc_human_db
+< 2024-12-16T15:31:53 jga_study-nbdc_human_db
togoid-config config/jga_study-nbdc_human_db update
-# Success: output/tsv/jga_study-nbdc_human_db.tsv is updated
-> 2024-12-06T20:44:16 jga_study-nbdc_human_db
+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
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: false
+task needed: true
timestamp: 2024-12-06 20:44:16 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 6.764153476198959 days ago (will be updated when >5 days)
+# File output/tsv/jga_study-pubmed.tsv is created 9.784533419575498 days ago (will be updated when >5 days)
## Update config/jga_study-pubmed/config.yaml => output/tsv/jga_study-pubmed.tsv
-< 2024-12-06T20:44:16 jga_study-pubmed
+< 2024-12-16T15:34:00 jga_study-pubmed
togoid-config config/jga_study-pubmed update
-# Success: output/tsv/jga_study-pubmed.tsv is updated
-> 2024-12-06T20:44:16 jga_study-pubmed
+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
Rule for TSV (output/tsv/jga_study-pubmed.tsv)
------------------------------
Investigating output/tsv/jga_study-pubmed.tsv
class: Rake::FileTask
-task needed: false
+task needed: true
timestamp: 2024-12-06 20:44:16 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 76.6774046462667 days ago (will be updated when >5 days)
+# File output/tsv/lipidmaps-chebi.tsv is created 86.46341337809038 days ago (will be updated when >5 days)
## Update config/lipidmaps-chebi/config.yaml => output/tsv/lipidmaps-chebi.tsv
-< 2024-12-06T20:44:16 lipidmaps-chebi
+< 2024-12-16T15:36:08 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
@@ -2460,7 +2333,7 @@ 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
-> 2024-12-06T20:44:19 lipidmaps-chebi
+> 2024-12-16T15:36:09 lipidmaps-chebi
Rule for TSV (output/tsv/lipidmaps-chebi.tsv)
------------------------------
Investigating output/tsv/lipidmaps-chebi.tsv
@@ -2469,16 +2342,16 @@ task needed: true
timestamp: 2024-09-21 04:28:49 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 76.67739327718776 days ago (will be updated when >5 days)
+# File output/tsv/lipidmaps-inchi_key.tsv is created 86.46338789144772 days ago (will be updated when >5 days)
## Update config/lipidmaps-inchi_key/config.yaml => output/tsv/lipidmaps-inchi_key.tsv
-< 2024-12-06T20:44:19 lipidmaps-inchi_key
+< 2024-12-16T15:36:09 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
@@ -2494,7 +2367,7 @@ 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
-> 2024-12-06T20:44:21 lipidmaps-inchi_key
+> 2024-12-16T15:36:11 lipidmaps-inchi_key
Rule for TSV (output/tsv/lipidmaps-inchi_key.tsv)
------------------------------
Investigating output/tsv/lipidmaps-inchi_key.tsv
@@ -2503,16 +2376,16 @@ task needed: true
timestamp: 2024-09-21 04:28:53 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 76.67737408887432 days ago (will be updated when >5 days)
+# File output/tsv/lipidmaps-swisslipids.tsv is created 86.46336879690553 days ago (will be updated when >5 days)
## Update config/lipidmaps-swisslipids/config.yaml => output/tsv/lipidmaps-swisslipids.tsv
-< 2024-12-06T20:44:21 lipidmaps-swisslipids
+< 2024-12-16T15:36:11 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
@@ -2528,7 +2401,7 @@ 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
-> 2024-12-06T20:44:22 lipidmaps-swisslipids
+> 2024-12-16T15:36:12 lipidmaps-swisslipids
Rule for TSV (output/tsv/lipidmaps-swisslipids.tsv)
------------------------------
Investigating output/tsv/lipidmaps-swisslipids.tsv
@@ -2537,21 +2410,21 @@ task needed: true
timestamp: 2024-09-21 04:28:56 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 48.94180978284225 days ago (will be updated when >5 days)
+# File output/tsv/mbgd_gene-uniprot.tsv is created 58.7278045114042 days ago (will be updated when >5 days)
## Update config/mbgd_gene-uniprot/config.yaml => output/tsv/mbgd_gene-uniprot.tsv
-< 2024-12-06T20:44:22 mbgd_gene-uniprot
+< 2024-12-16T15:36:12 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
-> 2024-12-06T20:44:25 mbgd_gene-uniprot
+> 2024-12-16T15:36:15 mbgd_gene-uniprot
Rule for TSV (output/tsv/mbgd_gene-uniprot.tsv)
------------------------------
Investigating output/tsv/mbgd_gene-uniprot.tsv
@@ -2560,21 +2433,21 @@ task needed: true
timestamp: 2024-10-18 22:08:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 48.941843749965535 days ago (will be updated when >5 days)
+# File output/tsv/mbgd_organism-taxonomy.tsv is created 58.72783958399594 days ago (will be updated when >5 days)
## Update config/mbgd_organism-taxonomy/config.yaml => output/tsv/mbgd_organism-taxonomy.tsv
-< 2024-12-06T20:44:25 mbgd_organism-taxonomy
+< 2024-12-16T15:36:15 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
-> 2024-12-06T20:44:28 mbgd_organism-taxonomy
+> 2024-12-16T15:36:18 mbgd_organism-taxonomy
Rule for TSV (output/tsv/mbgd_organism-taxonomy.tsv)
------------------------------
Investigating output/tsv/mbgd_organism-taxonomy.tsv
@@ -2583,275 +2456,307 @@ task needed: true
timestamp: 2024-10-18 22:08:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-hp_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764105146643876 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:28 medgen-hp_phenotype
+< 2024-12-16T15:36:18 medgen-hp_phenotype
togoid-config config/medgen-hp_phenotype update
# Success: output/tsv/medgen-hp_phenotype.tsv is updated
-> 2024-12-06T20:44:29 medgen-hp_phenotype
+> 2024-12-16T15:36:19 medgen-hp_phenotype
Rule for TSV (output/tsv/medgen-hp_phenotype.tsv)
------------------------------
Investigating output/tsv/medgen-hp_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:29 +0900
+timestamp: 2024-12-16 15:36:19 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764081518681875 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:29 medgen-mesh
+< 2024-12-16T15:36:19 medgen-mesh
togoid-config config/medgen-mesh update
# Success: output/tsv/medgen-mesh.tsv is updated
-> 2024-12-06T20:44:29 medgen-mesh
+> 2024-12-16T15:36:19 medgen-mesh
Rule for TSV (output/tsv/medgen-mesh.tsv)
------------------------------
Investigating output/tsv/medgen-mesh.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:29 +0900
+timestamp: 2024-12-16 15:36:19 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764072419441899 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:29 medgen-mondo
+< 2024-12-16T15:36:19 medgen-mondo
togoid-config config/medgen-mondo update
# Success: output/tsv/medgen-mondo.tsv is updated
-> 2024-12-06T20:44:30 medgen-mondo
+> 2024-12-16T15:36:20 medgen-mondo
Rule for TSV (output/tsv/medgen-mondo.tsv)
------------------------------
Investigating output/tsv/medgen-mondo.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:30 +0900
+timestamp: 2024-12-16 15:36:20 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764069157570637 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:30 medgen-ncbigene
+< 2024-12-16T15:36:20 medgen-ncbigene
togoid-config config/medgen-ncbigene update
# Success: output/tsv/medgen-ncbigene.tsv is updated
-> 2024-12-06T20:44:30 medgen-ncbigene
+> 2024-12-16T15:36:20 medgen-ncbigene
Rule for TSV (output/tsv/medgen-ncbigene.tsv)
------------------------------
Investigating output/tsv/medgen-ncbigene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:30 +0900
+timestamp: 2024-12-16 15:36:20 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7640616902970025 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:30 medgen-omim_phenotype
+< 2024-12-16T15:36:20 medgen-omim_phenotype
togoid-config config/medgen-omim_phenotype update
# Success: output/tsv/medgen-omim_phenotype.tsv is updated
-> 2024-12-06T20:44:30 medgen-omim_phenotype
+> 2024-12-16T15:36:21 medgen-omim_phenotype
Rule for TSV (output/tsv/medgen-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/medgen-omim_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:30 +0900
+timestamp: 2024-12-16 15:36:21 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for medgen-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764058673862384 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:30 medgen-orphanet_phenotype
+< 2024-12-16T15:36:21 medgen-orphanet_phenotype
togoid-config config/medgen-orphanet_phenotype update
# Success: output/tsv/medgen-orphanet_phenotype.tsv is updated
-> 2024-12-06T20:44:31 medgen-orphanet_phenotype
+> 2024-12-16T15:36:22 medgen-orphanet_phenotype
Rule for TSV (output/tsv/medgen-orphanet_phenotype.tsv)
------------------------------
Investigating output/tsv/medgen-orphanet_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:31 +0900
+timestamp: 2024-12-16 15:36:22 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
-### Update TSV for mgi_gene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_gene/download.lock
-# => Preserving output/tsv/mgi_gene-ensembl_gene.tsv
+# 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
+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
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: 2024-11-30 02:24:16 +0900
+timestamp: 2024-12-16 15:36:22 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_gene (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_gene (2024-12-16 15:36:22 +0900)
+latest-prerequisite time: 2024-12-16 15:36:22 +0900
................................
-### Update TSV for mgi_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_gene/download.lock
-# => Preserving output/tsv/mgi_gene-hgnc.tsv
+# 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
+togoid-config config/mgi_gene-hgnc update
+# Success: output/tsv/mgi_gene-hgnc.tsv is updated
+> 2024-12-16T15:36:23 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: 2024-11-30 02:24:17 +0900
+timestamp: 2024-12-16 15:36:23 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_gene (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_gene (2024-12-16 15:36:23 +0900)
+latest-prerequisite time: 2024-12-16 15:36:23 +0900
................................
-### Update TSV for mgi_gene-mgi_allele if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_gene/download.lock
-# => Preserving output/tsv/mgi_gene-mgi_allele.tsv
+# 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
+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
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: 2024-11-30 02:24:18 +0900
+timestamp: 2024-12-16 15:36:24 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_gene (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_gene (2024-12-16 15:36:24 +0900)
+latest-prerequisite time: 2024-12-16 15:36:24 +0900
................................
-### Update TSV for mgi_gene-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_gene/download.lock
-# => Preserving output/tsv/mgi_gene-ncbigene.tsv
+# 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
+togoid-config config/mgi_gene-ncbigene update
+# Success: output/tsv/mgi_gene-ncbigene.tsv is updated
+> 2024-12-16T15:36:25 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: 2024-11-30 02:24:19 +0900
+timestamp: 2024-12-16 15:36:25 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_gene (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_gene (2024-12-16 15:36:25 +0900)
+latest-prerequisite time: 2024-12-16 15:36:25 +0900
................................
-### Update TSV for mgi_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_gene/download.lock
-# => Preserving output/tsv/mgi_gene-uniprot.tsv
+# 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
+togoid-config config/mgi_gene-uniprot update
+# Success: output/tsv/mgi_gene-uniprot.tsv is updated
+> 2024-12-16T15:36:25 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: 2024-11-30 02:24:19 +0900
+timestamp: 2024-12-16 15:36:25 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_gene (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_gene (2024-12-16 15:36:25 +0900)
+latest-prerequisite time: 2024-12-16 15:36:25 +0900
................................
-### Update TSV for mgi_genotype-doid if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_genotype/download.lock
-# => Preserving output/tsv/mgi_genotype-doid.tsv
+# 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
+togoid-config config/mgi_genotype-doid update
+# Success: output/tsv/mgi_genotype-doid.tsv is updated
+> 2024-12-16T15:36:27 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: 2024-11-30 02:24:21 +0900
+timestamp: 2024-12-16 15:36:27 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_genotype (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_genotype (2024-12-16 15:36:27 +0900)
+latest-prerequisite time: 2024-12-16 15:36:27 +0900
................................
-### Update TSV for mgi_genotype-mgi_allele if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_genotype/download.lock
-# => Preserving output/tsv/mgi_genotype-mgi_allele.tsv
+# 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
+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
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: 2024-11-30 02:24:22 +0900
+timestamp: 2024-12-16 15:36:28 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_genotype (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_genotype (2024-12-16 15:36:28 +0900)
+latest-prerequisite time: 2024-12-16 15:36:28 +0900
................................
-### Update TSV for mgi_genotype-mp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
+### 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 newer than input/mgi_genotype/download.lock
-# => Preserving output/tsv/mgi_genotype-mp.tsv
+# 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
+togoid-config config/mgi_genotype-mp update
+# Success: output/tsv/mgi_genotype-mp.tsv is updated
+> 2024-12-16T15:36:31 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: 2024-11-30 02:24:24 +0900
+timestamp: 2024-12-16 15:36:31 +0900
pre-requisites:
--output/tsv/ ()
---prepare:mgi_genotype (2024-12-06 20:44:31 +0900)
-latest-prerequisite time: 2024-12-06 20:44:31 +0900
+--prepare:mgi_genotype (2024-12-16 15:36:31 +0900)
+latest-prerequisite time: 2024-12-16 15:36:31 +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 195.23317545258652 days ago (will be updated when >5 days)
+# File output/tsv/mondo-doid.tsv is created 205.01928578893052 days ago (will be updated when >5 days)
## Update config/mondo-doid/config.yaml => output/tsv/mondo-doid.tsv
-< 2024-12-06T20:44:31 mondo-doid
+< 2024-12-16T15:36:31 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
-> 2024-12-06T20:44:31 mondo-doid
+> 2024-12-16T15:36:31 mondo-doid
Rule for TSV (output/tsv/mondo-doid.tsv)
------------------------------
Investigating output/tsv/mondo-doid.tsv
@@ -2860,21 +2765,21 @@ task needed: true
timestamp: 2024-05-25 15:08:45 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 195.23317416705123 days ago (will be updated when >5 days)
+# File output/tsv/mondo-hp_phenotype.tsv is created 205.01928368365486 days ago (will be updated when >5 days)
## Update config/mondo-hp_phenotype/config.yaml => output/tsv/mondo-hp_phenotype.tsv
-< 2024-12-06T20:44:31 mondo-hp_phenotype
+< 2024-12-16T15:36:31 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
-> 2024-12-06T20:44:32 mondo-hp_phenotype
+> 2024-12-16T15:36:32 mondo-hp_phenotype
Rule for TSV (output/tsv/mondo-hp_phenotype.tsv)
------------------------------
Investigating output/tsv/mondo-hp_phenotype.tsv
@@ -2883,21 +2788,21 @@ task needed: true
timestamp: 2024-05-25 15:08:45 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 195.2331749877912 days ago (will be updated when >5 days)
+# File output/tsv/mondo-meddra.tsv is created 205.0192836662879 days ago (will be updated when >5 days)
## Update config/mondo-meddra/config.yaml => output/tsv/mondo-meddra.tsv
-< 2024-12-06T20:44:32 mondo-meddra
+< 2024-12-16T15:36:32 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
-> 2024-12-06T20:44:32 mondo-meddra
+> 2024-12-16T15:36:32 mondo-meddra
Rule for TSV (output/tsv/mondo-meddra.tsv)
------------------------------
Investigating output/tsv/mondo-meddra.tsv
@@ -2906,21 +2811,21 @@ task needed: true
timestamp: 2024-05-25 15:08:45 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 195.23317402975687 days ago (will be updated when >5 days)
+# File output/tsv/mondo-mesh.tsv is created 205.0192830672745 days ago (will be updated when >5 days)
## Update config/mondo-mesh/config.yaml => output/tsv/mondo-mesh.tsv
-< 2024-12-06T20:44:32 mondo-mesh
+< 2024-12-16T15:36:32 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
-> 2024-12-06T20:44:33 mondo-mesh
+> 2024-12-16T15:36:32 mondo-mesh
Rule for TSV (output/tsv/mondo-mesh.tsv)
------------------------------
Investigating output/tsv/mondo-mesh.tsv
@@ -2929,21 +2834,21 @@ task needed: true
timestamp: 2024-05-25 15:08:46 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 195.23317404142452 days ago (will be updated when >5 days)
+# File output/tsv/mondo-omim_phenotype.tsv is created 205.01928378979937 days ago (will be updated when >5 days)
## Update config/mondo-omim_phenotype/config.yaml => output/tsv/mondo-omim_phenotype.tsv
-< 2024-12-06T20:44:33 mondo-omim_phenotype
+< 2024-12-16T15:36:32 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
-> 2024-12-06T20:44:33 mondo-omim_phenotype
+> 2024-12-16T15:36:33 mondo-omim_phenotype
Rule for TSV (output/tsv/mondo-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/mondo-omim_phenotype.tsv
@@ -2952,21 +2857,21 @@ task needed: true
timestamp: 2024-05-25 15:08:46 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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 195.23317354703494 days ago (will be updated when >5 days)
+# File output/tsv/mondo-orphanet_phenotype.tsv is created 205.01928374080936 days ago (will be updated when >5 days)
## Update config/mondo-orphanet_phenotype/config.yaml => output/tsv/mondo-orphanet_phenotype.tsv
-< 2024-12-06T20:44:33 mondo-orphanet_phenotype
+< 2024-12-16T15:36:33 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
-> 2024-12-06T20:44:33 mondo-orphanet_phenotype
+> 2024-12-16T15:36:33 mondo-orphanet_phenotype
Rule for TSV (output/tsv/mondo-orphanet_phenotype.tsv)
------------------------------
Investigating output/tsv/mondo-orphanet_phenotype.tsv
@@ -2975,467 +2880,450 @@ task needed: true
timestamp: 2024-05-25 15:08:47 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for nando-mondo if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7639591698930435 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T20:44:33 nando-mondo
+< 2024-12-16T15:36:33 nando-mondo
togoid-config config/nando-mondo update
# Success: output/tsv/nando-mondo.tsv is updated
-> 2024-12-06T20:44:34 nando-mondo
+> 2024-12-16T15:36:34 nando-mondo
Rule for TSV (output/tsv/nando-mondo.tsv)
------------------------------
Investigating output/tsv/nando-mondo.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 20:44:34 +0900
+timestamp: 2024-12-16 15:36:34 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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
-< 2024-12-06T20:44:34 ncbigene-ensembl_gene
+< 2024-12-16T15:36:34 ncbigene-ensembl_gene
togoid-config config/ncbigene-ensembl_gene update
# Success: output/tsv/ncbigene-ensembl_gene.tsv is updated
-> 2024-12-06T20:45:12 ncbigene-ensembl_gene
+> 2024-12-16T15:37:09 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: 2024-12-06 20:45:12 +0900
+timestamp: 2024-12-16 15:37:09 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:45:12 +0900)
-latest-prerequisite time: 2024-12-06 20:45:12 +0900
+--prepare:ncbigene (2024-12-16 15:37:09 +0900)
+latest-prerequisite time: 2024-12-16 15:37:09 +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
-< 2024-12-06T20:45:12 ncbigene-ensembl_protein
+< 2024-12-16T15:37:09 ncbigene-ensembl_protein
togoid-config config/ncbigene-ensembl_protein update
# Success: output/tsv/ncbigene-ensembl_protein.tsv is updated
-> 2024-12-06T20:46:22 ncbigene-ensembl_protein
+> 2024-12-16T15:38:21 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: 2024-12-06 20:46:22 +0900
+timestamp: 2024-12-16 15:38:21 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:46:22 +0900)
-latest-prerequisite time: 2024-12-06 20:46:22 +0900
+--prepare:ncbigene (2024-12-16 15:38:21 +0900)
+latest-prerequisite time: 2024-12-16 15:38:21 +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
-< 2024-12-06T20:46:22 ncbigene-ensembl_transcript
+< 2024-12-16T15:38:21 ncbigene-ensembl_transcript
togoid-config config/ncbigene-ensembl_transcript update
# Success: output/tsv/ncbigene-ensembl_transcript.tsv is updated
-> 2024-12-06T20:47:27 ncbigene-ensembl_transcript
+> 2024-12-16T15:39:28 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: 2024-12-06 20:47:27 +0900
+timestamp: 2024-12-16 15:39:28 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:47:27 +0900)
-latest-prerequisite time: 2024-12-06 20:47:27 +0900
+--prepare:ncbigene (2024-12-16 15:39:28 +0900)
+latest-prerequisite time: 2024-12-16 15:39:28 +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
-< 2024-12-06T20:47:27 ncbigene-flybase_gene
+< 2024-12-16T15:39:28 ncbigene-flybase_gene
togoid-config config/ncbigene-flybase_gene update
# Success: output/tsv/ncbigene-flybase_gene.tsv is updated
-> 2024-12-06T20:48:59 ncbigene-flybase_gene
+> 2024-12-16T15:40:51 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: 2024-12-06 20:48:59 +0900
+timestamp: 2024-12-16 15:40:51 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:48:59 +0900)
-latest-prerequisite time: 2024-12-06 20:48:59 +0900
+--prepare:ncbigene (2024-12-16 15:40:51 +0900)
+latest-prerequisite time: 2024-12-16 15:40:51 +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
-< 2024-12-06T20:48:59 ncbigene-go
+< 2024-12-16T15:40:51 ncbigene-go
togoid-config config/ncbigene-go update
# Success: output/tsv/ncbigene-go.tsv is updated
-> 2024-12-06T20:55:55 ncbigene-go
+> 2024-12-16T15:47:16 ncbigene-go
Rule for TSV (output/tsv/ncbigene-go.tsv)
------------------------------
Investigating output/tsv/ncbigene-go.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:55:55 +0900
+timestamp: 2024-12-16 15:47:16 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:55:55 +0900)
-latest-prerequisite time: 2024-12-06 20:55:55 +0900
+--prepare:ncbigene (2024-12-16 15:47:16 +0900)
+latest-prerequisite time: 2024-12-16 15:47:16 +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
-< 2024-12-06T20:55:55 ncbigene-hgnc
+< 2024-12-16T15:47:16 ncbigene-hgnc
togoid-config config/ncbigene-hgnc update
# Success: output/tsv/ncbigene-hgnc.tsv is updated
-> 2024-12-06T20:55:56 ncbigene-hgnc
+> 2024-12-16T15:47:17 ncbigene-hgnc
Rule for TSV (output/tsv/ncbigene-hgnc.tsv)
------------------------------
Investigating output/tsv/ncbigene-hgnc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:55:56 +0900
+timestamp: 2024-12-16 15:47:17 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:55:56 +0900)
-latest-prerequisite time: 2024-12-06 20:55:56 +0900
+--prepare:ncbigene (2024-12-16 15:47:17 +0900)
+latest-prerequisite time: 2024-12-16 15:47:17 +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
-< 2024-12-06T20:55:56 ncbigene-mgi_gene
+< 2024-12-16T15:47:17 ncbigene-mgi_gene
togoid-config config/ncbigene-mgi_gene update
# Success: output/tsv/ncbigene-mgi_gene.tsv is updated
-> 2024-12-06T20:57:04 ncbigene-mgi_gene
+> 2024-12-16T15:48:26 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: 2024-12-06 20:57:04 +0900
+timestamp: 2024-12-16 15:48:26 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:57:04 +0900)
-latest-prerequisite time: 2024-12-06 20:57:04 +0900
+--prepare:ncbigene (2024-12-16 15:48:26 +0900)
+latest-prerequisite time: 2024-12-16 15:48:26 +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
-< 2024-12-06T20:57:04 ncbigene-mirbase
+< 2024-12-16T15:48:26 ncbigene-mirbase
togoid-config config/ncbigene-mirbase update
# Success: output/tsv/ncbigene-mirbase.tsv is updated
-> 2024-12-06T20:59:00 ncbigene-mirbase
+> 2024-12-16T15:50:19 ncbigene-mirbase
Rule for TSV (output/tsv/ncbigene-mirbase.tsv)
------------------------------
Investigating output/tsv/ncbigene-mirbase.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 20:59:00 +0900
+timestamp: 2024-12-16 15:50:19 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:59:00 +0900)
-latest-prerequisite time: 2024-12-06 20:59:00 +0900
+--prepare:ncbigene (2024-12-16 15:50:19 +0900)
+latest-prerequisite time: 2024-12-16 15:50:19 +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
-< 2024-12-06T20:59:00 ncbigene-omim_gene
+< 2024-12-16T15:50:19 ncbigene-omim_gene
togoid-config config/ncbigene-omim_gene update
# Success: output/tsv/ncbigene-omim_gene.tsv is updated
-> 2024-12-06T20:59:01 ncbigene-omim_gene
+> 2024-12-16T15:50:20 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: 2024-12-06 20:59:01 +0900
+timestamp: 2024-12-16 15:50:20 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 20:59:01 +0900)
-latest-prerequisite time: 2024-12-06 20:59:01 +0900
+--prepare:ncbigene (2024-12-16 15:50:20 +0900)
+latest-prerequisite time: 2024-12-16 15:50:20 +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
-< 2024-12-06T20:59:01 ncbigene-refseq_genomic
+< 2024-12-16T15:50:20 ncbigene-refseq_genomic
togoid-config config/ncbigene-refseq_genomic update
# Success: output/tsv/ncbigene-refseq_genomic.tsv is updated
-> 2024-12-06T21:03:27 ncbigene-refseq_genomic
+> 2024-12-16T15:55:05 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: 2024-12-06 21:03:27 +0900
+timestamp: 2024-12-16 15:55:05 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:03:27 +0900)
-latest-prerequisite time: 2024-12-06 21:03:27 +0900
+--prepare:ncbigene (2024-12-16 15:55:05 +0900)
+latest-prerequisite time: 2024-12-16 15:55:05 +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
-< 2024-12-06T21:03:27 ncbigene-refseq_protein
+< 2024-12-16T15:55:05 ncbigene-refseq_protein
togoid-config config/ncbigene-refseq_protein update
# Success: output/tsv/ncbigene-refseq_protein.tsv is updated
-> 2024-12-06T21:08:16 ncbigene-refseq_protein
+> 2024-12-16T16:00:30 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: 2024-12-06 21:08:16 +0900
+timestamp: 2024-12-16 16:00:30 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:08:16 +0900)
-latest-prerequisite time: 2024-12-06 21:08:16 +0900
+--prepare:ncbigene (2024-12-16 16:00:30 +0900)
+latest-prerequisite time: 2024-12-16 16:00:30 +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
-< 2024-12-06T21:08:16 ncbigene-refseq_rna
+< 2024-12-16T16:00:30 ncbigene-refseq_rna
togoid-config config/ncbigene-refseq_rna update
# Success: output/tsv/ncbigene-refseq_rna.tsv is updated
-> 2024-12-06T21:12:28 ncbigene-refseq_rna
+> 2024-12-16T16:05:07 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: 2024-12-06 21:12:28 +0900
+timestamp: 2024-12-16 16:05:07 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:12:28 +0900)
-latest-prerequisite time: 2024-12-06 21:12:28 +0900
+--prepare:ncbigene (2024-12-16 16:05:07 +0900)
+latest-prerequisite time: 2024-12-16 16:05:07 +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
-< 2024-12-06T21:12:28 ncbigene-rgd
+< 2024-12-16T16:05:07 ncbigene-rgd
togoid-config config/ncbigene-rgd update
# Success: output/tsv/ncbigene-rgd.tsv is updated
-> 2024-12-06T21:13:37 ncbigene-rgd
+> 2024-12-16T16:06:15 ncbigene-rgd
Rule for TSV (output/tsv/ncbigene-rgd.tsv)
------------------------------
Investigating output/tsv/ncbigene-rgd.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:13:37 +0900
+timestamp: 2024-12-16 16:06:15 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:13:37 +0900)
-latest-prerequisite time: 2024-12-06 21:13:37 +0900
+--prepare:ncbigene (2024-12-16 16:06:15 +0900)
+latest-prerequisite time: 2024-12-16 16:06:15 +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
-< 2024-12-06T21:13:37 ncbigene-sgd
+< 2024-12-16T16:06:15 ncbigene-sgd
togoid-config config/ncbigene-sgd update
# Success: output/tsv/ncbigene-sgd.tsv is updated
-> 2024-12-06T21:14:56 ncbigene-sgd
+> 2024-12-16T16:07:34 ncbigene-sgd
Rule for TSV (output/tsv/ncbigene-sgd.tsv)
------------------------------
Investigating output/tsv/ncbigene-sgd.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:14:56 +0900
+timestamp: 2024-12-16 16:07:34 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:14:56 +0900)
-latest-prerequisite time: 2024-12-06 21:14:56 +0900
+--prepare:ncbigene (2024-12-16 16:07:34 +0900)
+latest-prerequisite time: 2024-12-16 16:07:34 +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
-< 2024-12-06T21:14:56 ncbigene-tair
+< 2024-12-16T16:07:34 ncbigene-tair
togoid-config config/ncbigene-tair update
# Success: output/tsv/ncbigene-tair.tsv is updated
-> 2024-12-06T21:16:14 ncbigene-tair
+> 2024-12-16T16:08:52 ncbigene-tair
Rule for TSV (output/tsv/ncbigene-tair.tsv)
------------------------------
Investigating output/tsv/ncbigene-tair.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:16:14 +0900
+timestamp: 2024-12-16 16:08:52 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:16:14 +0900)
-latest-prerequisite time: 2024-12-06 21:16:14 +0900
+--prepare:ncbigene (2024-12-16 16:08:52 +0900)
+latest-prerequisite time: 2024-12-16 16:08:52 +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
-< 2024-12-06T21:16:14 ncbigene-taxonomy
+< 2024-12-16T16:08:52 ncbigene-taxonomy
togoid-config config/ncbigene-taxonomy update
# Success: output/tsv/ncbigene-taxonomy.tsv is updated
-> 2024-12-06T21:17:02 ncbigene-taxonomy
+> 2024-12-16T16:09:42 ncbigene-taxonomy
Rule for TSV (output/tsv/ncbigene-taxonomy.tsv)
------------------------------
Investigating output/tsv/ncbigene-taxonomy.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:17:02 +0900
+timestamp: 2024-12-16 16:09:42 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:17:02 +0900)
-latest-prerequisite time: 2024-12-06 21:17:02 +0900
+--prepare:ncbigene (2024-12-16 16:09:42 +0900)
+latest-prerequisite time: 2024-12-16 16:09:42 +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
-< 2024-12-06T21:17:02 ncbigene-vgnc
+< 2024-12-16T16:09:42 ncbigene-vgnc
togoid-config config/ncbigene-vgnc update
# Success: output/tsv/ncbigene-vgnc.tsv is updated
-> 2024-12-06T21:18:23 ncbigene-vgnc
+> 2024-12-16T16:11:01 ncbigene-vgnc
Rule for TSV (output/tsv/ncbigene-vgnc.tsv)
------------------------------
Investigating output/tsv/ncbigene-vgnc.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:18:23 +0900
+timestamp: 2024-12-16 16:11:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:18:23 +0900)
-latest-prerequisite time: 2024-12-06 21:18:23 +0900
+--prepare:ncbigene (2024-12-16 16:11:01 +0900)
+latest-prerequisite time: 2024-12-16 16:11:01 +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
-< 2024-12-06T21:18:23 ncbigene-wormbase_gene
+< 2024-12-16T16:11:01 ncbigene-wormbase_gene
togoid-config config/ncbigene-wormbase_gene update
# Success: output/tsv/ncbigene-wormbase_gene.tsv is updated
-> 2024-12-06T21:19:41 ncbigene-wormbase_gene
+> 2024-12-16T16:12:20 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: 2024-12-06 21:19:41 +0900
+timestamp: 2024-12-16 16:12:20 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:19:41 +0900)
-latest-prerequisite time: 2024-12-06 21:19:41 +0900
+--prepare:ncbigene (2024-12-16 16:12:20 +0900)
+latest-prerequisite time: 2024-12-16 16:12:20 +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
-< 2024-12-06T21:19:41 ncbigene-xenbase_gene
+< 2024-12-16T16:12:20 ncbigene-xenbase_gene
togoid-config config/ncbigene-xenbase_gene update
# Success: output/tsv/ncbigene-xenbase_gene.tsv is updated
-> 2024-12-06T21:20:59 ncbigene-xenbase_gene
+> 2024-12-16T16:13:38 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: 2024-12-06 21:20:59 +0900
+timestamp: 2024-12-16 16:13:38 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:20:59 +0900)
-latest-prerequisite time: 2024-12-06 21:20:59 +0900
+--prepare:ncbigene (2024-12-16 16:13:38 +0900)
+latest-prerequisite time: 2024-12-16 16:13:38 +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
-< 2024-12-06T21:20:59 ncbigene-zfin_gene
+< 2024-12-16T16:13:38 ncbigene-zfin_gene
togoid-config config/ncbigene-zfin_gene update
# Success: output/tsv/ncbigene-zfin_gene.tsv is updated
-> 2024-12-06T21:22:16 ncbigene-zfin_gene
+> 2024-12-16T16:14:56 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: 2024-12-06 21:22:16 +0900
+timestamp: 2024-12-16 16:14:56 +0900
pre-requisites:
--output/tsv/ ()
---prepare:ncbigene (2024-12-06 21:22:16 +0900)
-latest-prerequisite time: 2024-12-06 21:22:16 +0900
+--prepare:ncbigene (2024-12-16 16:14:56 +0900)
+latest-prerequisite time: 2024-12-16 16:14:56 +0900
................................
### Update TSV for ncit_disease-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764404379037547 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:22:16 ncit_disease-ncit_tissue
+< 2024-12-16T16:14:56 ncit_disease-ncit_tissue
togoid-config config/ncit_disease-ncit_tissue update
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv new file size per old 291 / 385314 = 0.0007552282034911786 < 0.5
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML 408 Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Server timeout waiting for the HTTP request from the client.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Additionally a 502 Bad Gateway
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML 408 Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Request Timeout
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Server timeout waiting for the HTTP request from the client.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML Additionally a 502 Bad Gateway
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.
-# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML
-# Failure: output/tsv/ncit_disease-ncit_tissue.tsv is not updated
-> 2024-12-06T21:24:32 ncit_disease-ncit_tissue
+# Success: output/tsv/ncit_disease-ncit_tissue.tsv is updated
+> 2024-12-16T16:15:00 ncit_disease-ncit_tissue
Rule for TSV (output/tsv/ncit_disease-ncit_tissue.tsv)
------------------------------
Investigating output/tsv/ncit_disease-ncit_tissue.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 03:01:32 +0900
+task needed: false
+timestamp: 2024-12-16 16:15:00 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for oma_protein-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -3450,8 +3338,8 @@ task needed: true
timestamp: 2024-09-27 22:31:53 +0900
pre-requisites:
--output/tsv/ ()
---prepare:oma_protein (2024-12-06 21:24:32 +0900)
-latest-prerequisite time: 2024-12-06 21:24:32 +0900
+--prepare:oma_protein (2024-12-16 16:15:00 +0900)
+latest-prerequisite time: 2024-12-16 16:15:00 +0900
................................
### Update TSV for oma_protein-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -3466,8 +3354,8 @@ task needed: true
timestamp: 2024-09-27 22:39:06 +0900
pre-requisites:
--output/tsv/ ()
---prepare:oma_protein (2024-12-06 21:24:32 +0900)
-latest-prerequisite time: 2024-12-06 21:24:32 +0900
+--prepare:oma_protein (2024-12-16 16:15:00 +0900)
+latest-prerequisite time: 2024-12-16 16:15:00 +0900
................................
### Update TSV for oma_protein-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -3482,8 +3370,8 @@ task needed: true
timestamp: 2024-09-27 22:39:32 +0900
pre-requisites:
--output/tsv/ ()
---prepare:oma_protein (2024-12-06 21:24:32 +0900)
-latest-prerequisite time: 2024-12-06 21:24:32 +0900
+--prepare:oma_protein (2024-12-16 16:15:00 +0900)
+latest-prerequisite time: 2024-12-16 16:15:00 +0900
................................
### Update TSV for oma_protein-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -3498,301 +3386,301 @@ task needed: true
timestamp: 2024-09-27 22:39:39 +0900
pre-requisites:
--output/tsv/ ()
---prepare:oma_protein (2024-12-06 21:24:32 +0900)
-latest-prerequisite time: 2024-12-06 21:24:32 +0900
+--prepare:oma_protein (2024-12-16 16:15:00 +0900)
+latest-prerequisite time: 2024-12-16 16:15:00 +0900
................................
### Update TSV for orphanet_gene-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.76597214841875 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:32 orphanet_gene-ensembl_gene
+< 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
-> 2024-12-06T21:24:33 orphanet_gene-ensembl_gene
+> 2024-12-16T16:15:01 orphanet_gene-ensembl_gene
Rule for TSV (output/tsv/orphanet_gene-ensembl_gene.tsv)
------------------------------
Investigating output/tsv/orphanet_gene-ensembl_gene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:33 +0900
+timestamp: 2024-12-16 16:15:01 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_gene-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765972078040683 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:33 orphanet_gene-hgnc
+< 2024-12-16T16:15:01 orphanet_gene-hgnc
togoid-config config/orphanet_gene-hgnc update
# Success: output/tsv/orphanet_gene-hgnc.tsv is updated
-> 2024-12-06T21:24:33 orphanet_gene-hgnc
+> 2024-12-16T16:15:01 orphanet_gene-hgnc
Rule for TSV (output/tsv/orphanet_gene-hgnc.tsv)
------------------------------
Investigating output/tsv/orphanet_gene-hgnc.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:33 +0900
+timestamp: 2024-12-16 16:15:01 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_gene-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765970192182257 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:33 orphanet_gene-omim_gene
+< 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
-> 2024-12-06T21:24:33 orphanet_gene-omim_gene
+> 2024-12-16T16:15:02 orphanet_gene-omim_gene
Rule for TSV (output/tsv/orphanet_gene-omim_gene.tsv)
------------------------------
Investigating output/tsv/orphanet_gene-omim_gene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:33 +0900
+timestamp: 2024-12-16 16:15:02 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_gene-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765960027227373 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:33 orphanet_gene-uniprot
+< 2024-12-16T16:15:02 orphanet_gene-uniprot
togoid-config config/orphanet_gene-uniprot update
# Success: output/tsv/orphanet_gene-uniprot.tsv is updated
-> 2024-12-06T21:24:34 orphanet_gene-uniprot
+> 2024-12-16T16:15:02 orphanet_gene-uniprot
Rule for TSV (output/tsv/orphanet_gene-uniprot.tsv)
------------------------------
Investigating output/tsv/orphanet_gene-uniprot.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:34 +0900
+timestamp: 2024-12-16 16:15:02 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_phenotype-meddra if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.76594938071397 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:34 orphanet_phenotype-meddra
+< 2024-12-16T16:15:02 orphanet_phenotype-meddra
togoid-config config/orphanet_phenotype-meddra update
# Success: output/tsv/orphanet_phenotype-meddra.tsv is updated
-> 2024-12-06T21:24:34 orphanet_phenotype-meddra
+> 2024-12-16T16:15:02 orphanet_phenotype-meddra
Rule for TSV (output/tsv/orphanet_phenotype-meddra.tsv)
------------------------------
Investigating output/tsv/orphanet_phenotype-meddra.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:34 +0900
+timestamp: 2024-12-16 16:15:02 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_phenotype-mesh if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765943117090798 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:34 orphanet_phenotype-mesh
+< 2024-12-16T16:15:02 orphanet_phenotype-mesh
togoid-config config/orphanet_phenotype-mesh update
# Success: output/tsv/orphanet_phenotype-mesh.tsv is updated
-> 2024-12-06T21:24:35 orphanet_phenotype-mesh
+> 2024-12-16T16:15:03 orphanet_phenotype-mesh
Rule for TSV (output/tsv/orphanet_phenotype-mesh.tsv)
------------------------------
Investigating output/tsv/orphanet_phenotype-mesh.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:35 +0900
+timestamp: 2024-12-16 16:15:03 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_phenotype-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7659428123514695 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:35 orphanet_phenotype-omim_phenotype
+< 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
-> 2024-12-06T21:24:35 orphanet_phenotype-omim_phenotype
+> 2024-12-16T16:15:03 orphanet_phenotype-omim_phenotype
Rule for TSV (output/tsv/orphanet_phenotype-omim_phenotype.tsv)
------------------------------
Investigating output/tsv/orphanet_phenotype-omim_phenotype.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:35 +0900
+timestamp: 2024-12-16 16:15:03 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for orphanet_phenotype-orphanet_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765943029974734 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:35 orphanet_phenotype-orphanet_gene
+< 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
-> 2024-12-06T21:24:36 orphanet_phenotype-orphanet_gene
+> 2024-12-16T16:15:04 orphanet_phenotype-orphanet_gene
Rule for TSV (output/tsv/orphanet_phenotype-orphanet_gene.tsv)
------------------------------
Investigating output/tsv/orphanet_phenotype-orphanet_gene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:36 +0900
+timestamp: 2024-12-16 16:15:04 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pdb-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765900584318958 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:36 pdb-go
+< 2024-12-16T16:15:04 pdb-go
togoid-config config/pdb-go update
# Success: output/tsv/pdb-go.tsv is updated
-> 2024-12-06T21:24:40 pdb-go
+> 2024-12-16T16:15:08 pdb-go
Rule for TSV (output/tsv/pdb-go.tsv)
------------------------------
Investigating output/tsv/pdb-go.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:40 +0900
+timestamp: 2024-12-16 16:15:08 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pdb-interpro if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765928261998148 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:40 pdb-interpro
+< 2024-12-16T16:15:08 pdb-interpro
togoid-config config/pdb-interpro update
# Success: output/tsv/pdb-interpro.tsv is updated
-> 2024-12-06T21:24:41 pdb-interpro
+> 2024-12-16T16:15:10 pdb-interpro
Rule for TSV (output/tsv/pdb-interpro.tsv)
------------------------------
Investigating output/tsv/pdb-interpro.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:41 +0900
+timestamp: 2024-12-16 16:15:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pdb-pdb_ccd if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765932169875394 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:41 pdb-pdb_ccd
+< 2024-12-16T16:15:10 pdb-pdb_ccd
togoid-config config/pdb-pdb_ccd update
# Success: output/tsv/pdb-pdb_ccd.tsv is updated
-> 2024-12-06T21:24:42 pdb-pdb_ccd
+> 2024-12-16T16:15:11 pdb-pdb_ccd
Rule for TSV (output/tsv/pdb-pdb_ccd.tsv)
------------------------------
Investigating output/tsv/pdb-pdb_ccd.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:42 +0900
+timestamp: 2024-12-16 16:15:11 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pdb-pfam if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765934516571239 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:42 pdb-pfam
+< 2024-12-16T16:15:11 pdb-pfam
togoid-config config/pdb-pfam update
# Success: output/tsv/pdb-pfam.tsv is updated
-> 2024-12-06T21:24:43 pdb-pfam
+> 2024-12-16T16:15:12 pdb-pfam
Rule for TSV (output/tsv/pdb-pfam.tsv)
------------------------------
Investigating output/tsv/pdb-pfam.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:43 +0900
+timestamp: 2024-12-16 16:15:12 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pdb-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765935512080347 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:24:43 pdb-uniprot
+< 2024-12-16T16:15:12 pdb-uniprot
togoid-config config/pdb-uniprot update
# Success: output/tsv/pdb-uniprot.tsv is updated
-> 2024-12-06T21:24:44 pdb-uniprot
+> 2024-12-16T16:15:13 pdb-uniprot
Rule for TSV (output/tsv/pdb-uniprot.tsv)
------------------------------
Investigating output/tsv/pdb-uniprot.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:24:44 +0900
+timestamp: 2024-12-16 16:15:13 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +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
-< 2024-12-06T21:24:44 pmc-pubmed
+< 2024-12-16T16:15:13 pmc-pubmed
togoid-config config/pmc-pubmed update
# Success: output/tsv/pmc-pubmed.tsv is updated
-> 2024-12-06T21:30:33 pmc-pubmed
+> 2024-12-16T16:21:00 pmc-pubmed
Rule for TSV (output/tsv/pmc-pubmed.tsv)
------------------------------
Investigating output/tsv/pmc-pubmed.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:30:33 +0900
+timestamp: 2024-12-16 16:21:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:pmc (2024-12-06 21:30:33 +0900)
-latest-prerequisite time: 2024-12-06 21:30:33 +0900
+--prepare:pmc (2024-12-16 16:21:00 +0900)
+latest-prerequisite time: 2024-12-16 16:21:00 +0900
................................
### Update TSV for prosite-prosite_prorule if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -3807,511 +3695,511 @@ task needed: true
timestamp: 2024-11-30 03:07:42 +0900
pre-requisites:
--output/tsv/ ()
---prepare:prosite (2024-12-06 21:30:33 +0900)
-latest-prerequisite time: 2024-12-06 21:30:33 +0900
+--prepare:prosite (2024-12-16 16:21:00 +0900)
+latest-prerequisite time: 2024-12-16 16:21:00 +0900
................................
### Update TSV for pubchem_compound-atc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765866198927408 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:33 pubchem_compound-atc
+< 2024-12-16T16:21:00 pubchem_compound-atc
togoid-config config/pubchem_compound-atc update
# Success: output/tsv/pubchem_compound-atc.tsv is updated
-> 2024-12-06T21:30:34 pubchem_compound-atc
+> 2024-12-16T16:21:00 pubchem_compound-atc
Rule for TSV (output/tsv/pubchem_compound-atc.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-atc.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:30:34 +0900
+timestamp: 2024-12-16 16:21:00 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_compound-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765862951766285 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:34 pubchem_compound-chebi
+< 2024-12-16T16:21:00 pubchem_compound-chebi
togoid-config config/pubchem_compound-chebi update
# Success: output/tsv/pubchem_compound-chebi.tsv is updated
-> 2024-12-06T21:30:34 pubchem_compound-chebi
+> 2024-12-16T16:21:01 pubchem_compound-chebi
Rule for TSV (output/tsv/pubchem_compound-chebi.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-chebi.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:30:34 +0900
+timestamp: 2024-12-16 16:21:01 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_compound-chembl_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7658121397908335 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:34 pubchem_compound-chembl_compound
+< 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
-> 2024-12-06T21:30:39 pubchem_compound-chembl_compound
+> 2024-12-16T16:21:06 pubchem_compound-chembl_compound
Rule for TSV (output/tsv/pubchem_compound-chembl_compound.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-chembl_compound.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:30:39 +0900
+timestamp: 2024-12-16 16:21:06 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_compound-drugbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765864182556563 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:39 pubchem_compound-drugbank
+< 2024-12-16T16:21:06 pubchem_compound-drugbank
togoid-config config/pubchem_compound-drugbank update
# Success: output/tsv/pubchem_compound-drugbank.tsv is updated
-> 2024-12-06T21:30:40 pubchem_compound-drugbank
+> 2024-12-16T16:21:06 pubchem_compound-drugbank
Rule for TSV (output/tsv/pubchem_compound-drugbank.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-drugbank.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:30:40 +0900
+timestamp: 2024-12-16 16:21:06 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_compound-glytoucan if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7658626854621415 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:40 pubchem_compound-glytoucan
+< 2024-12-16T16:21:06 pubchem_compound-glytoucan
togoid-config config/pubchem_compound-glytoucan update
# Success: output/tsv/pubchem_compound-glytoucan.tsv is updated
-> 2024-12-06T21:30:40 pubchem_compound-glytoucan
+> 2024-12-16T16:21:07 pubchem_compound-glytoucan
Rule for TSV (output/tsv/pubchem_compound-glytoucan.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-glytoucan.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:30:40 +0900
+timestamp: 2024-12-16 16:21:07 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_compound-inchi_key if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.760066873040127 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:30:40 pubchem_compound-inchi_key
+< 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
-> 2024-12-06T21:39:43 pubchem_compound-inchi_key
+> 2024-12-16T16:27:49 pubchem_compound-inchi_key
Rule for TSV (output/tsv/pubchem_compound-inchi_key.tsv)
------------------------------
Investigating output/tsv/pubchem_compound-inchi_key.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:43 +0900
+timestamp: 2024-12-16 16:27:49 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766337995704919 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:43 pubchem_pathway-ncbigene
+< 2024-12-16T16:27:49 pubchem_pathway-ncbigene
togoid-config config/pubchem_pathway-ncbigene update
# Success: output/tsv/pubchem_pathway-ncbigene.tsv is updated
-> 2024-12-06T21:39:43 pubchem_pathway-ncbigene
+> 2024-12-16T16:27:49 pubchem_pathway-ncbigene
Rule for TSV (output/tsv/pubchem_pathway-ncbigene.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-ncbigene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:43 +0900
+timestamp: 2024-12-16 16:27:49 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-pathbank if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766339629535451 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:43 pubchem_pathway-pathbank
+< 2024-12-16T16:27:49 pubchem_pathway-pathbank
togoid-config config/pubchem_pathway-pathbank update
# Success: output/tsv/pubchem_pathway-pathbank.tsv is updated
-> 2024-12-06T21:39:44 pubchem_pathway-pathbank
+> 2024-12-16T16:27:50 pubchem_pathway-pathbank
Rule for TSV (output/tsv/pubchem_pathway-pathbank.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-pathbank.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:44 +0900
+timestamp: 2024-12-16 16:27:50 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-pubchem_compound if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766313830657511 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:44 pubchem_pathway-pubchem_compound
+< 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
-> 2024-12-06T21:39:46 pubchem_pathway-pubchem_compound
+> 2024-12-16T16:27:52 pubchem_pathway-pubchem_compound
Rule for TSV (output/tsv/pubchem_pathway-pubchem_compound.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-pubchem_compound.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:46 +0900
+timestamp: 2024-12-16 16:27:52 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.76633994599618 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:46 pubchem_pathway-reactome_pathway
+< 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
-> 2024-12-06T21:39:47 pubchem_pathway-reactome_pathway
+> 2024-12-16T16:27:53 pubchem_pathway-reactome_pathway
Rule for TSV (output/tsv/pubchem_pathway-reactome_pathway.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-reactome_pathway.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:47 +0900
+timestamp: 2024-12-16 16:27:52 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766326350199281 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:47 pubchem_pathway-uniprot
+< 2024-12-16T16:27:53 pubchem_pathway-uniprot
togoid-config config/pubchem_pathway-uniprot update
# Success: output/tsv/pubchem_pathway-uniprot.tsv is updated
-> 2024-12-06T21:39:48 pubchem_pathway-uniprot
+> 2024-12-16T16:27:54 pubchem_pathway-uniprot
Rule for TSV (output/tsv/pubchem_pathway-uniprot.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-uniprot.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:48 +0900
+timestamp: 2024-12-16 16:27:54 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for pubchem_pathway-wikipathways if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766338466548623 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:48 pubchem_pathway-wikipathways
+< 2024-12-16T16:27:54 pubchem_pathway-wikipathways
togoid-config config/pubchem_pathway-wikipathways update
# Success: output/tsv/pubchem_pathway-wikipathways.tsv is updated
-> 2024-12-06T21:39:49 pubchem_pathway-wikipathways
+> 2024-12-16T16:27:54 pubchem_pathway-wikipathways
Rule for TSV (output/tsv/pubchem_pathway-wikipathways.tsv)
------------------------------
Investigating output/tsv/pubchem_pathway-wikipathways.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 21:39:49 +0900
+timestamp: 2024-12-16 16:27:54 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for reactome_pathway-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766329443593727 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:49 reactome_pathway-chebi
+< 2024-12-16T16:27:54 reactome_pathway-chebi
togoid-config config/reactome_pathway-chebi update
# Success: output/tsv/reactome_pathway-chebi.tsv is updated
-> 2024-12-06T21:39:49 reactome_pathway-chebi
+> 2024-12-16T16:27:55 reactome_pathway-chebi
Rule for TSV (output/tsv/reactome_pathway-chebi.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-chebi.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:49 +0900
+timestamp: 2024-12-16 16:27:55 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:49 +0900)
-latest-prerequisite time: 2024-12-06 21:39:49 +0900
+--prepare:reactome (2024-12-16 16:27:55 +0900)
+latest-prerequisite time: 2024-12-16 16:27:55 +0900
................................
### Update TSV for reactome_pathway-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7663303383564815 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:49 reactome_pathway-go
+< 2024-12-16T16:27:55 reactome_pathway-go
togoid-config config/reactome_pathway-go update
# Success: output/tsv/reactome_pathway-go.tsv is updated
-> 2024-12-06T21:39:50 reactome_pathway-go
+> 2024-12-16T16:27:55 reactome_pathway-go
Rule for TSV (output/tsv/reactome_pathway-go.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-go.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:50 +0900
+timestamp: 2024-12-16 16:27:55 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:50 +0900)
-latest-prerequisite time: 2024-12-06 21:39:50 +0900
+--prepare:reactome (2024-12-16 16:27:55 +0900)
+latest-prerequisite time: 2024-12-16 16:27:55 +0900
................................
### Update TSV for reactome_pathway-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766331017110821 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:50 reactome_pathway-iuphar_ligand
+< 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
-> 2024-12-06T21:39:50 reactome_pathway-iuphar_ligand
+> 2024-12-16T16:27:56 reactome_pathway-iuphar_ligand
Rule for TSV (output/tsv/reactome_pathway-iuphar_ligand.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-iuphar_ligand.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:50 +0900
+timestamp: 2024-12-16 16:27:56 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:50 +0900)
-latest-prerequisite time: 2024-12-06 21:39:50 +0900
+--prepare:reactome (2024-12-16 16:27:56 +0900)
+latest-prerequisite time: 2024-12-16 16:27:56 +0900
................................
### Update TSV for reactome_pathway-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766332260438542 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:50 reactome_pathway-mirbase
+< 2024-12-16T16:27:56 reactome_pathway-mirbase
togoid-config config/reactome_pathway-mirbase update
# Success: output/tsv/reactome_pathway-mirbase.tsv is updated
-> 2024-12-06T21:39:50 reactome_pathway-mirbase
+> 2024-12-16T16:27:56 reactome_pathway-mirbase
Rule for TSV (output/tsv/reactome_pathway-mirbase.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-mirbase.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:50 +0900
+timestamp: 2024-12-16 16:27:56 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:50 +0900)
-latest-prerequisite time: 2024-12-06 21:39:50 +0900
+--prepare:reactome (2024-12-16 16:27:56 +0900)
+latest-prerequisite time: 2024-12-16 16:27:56 +0900
................................
### Update TSV for reactome_pathway-reactome_reaction if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766321059861911 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:50 reactome_pathway-reactome_reaction
+< 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
-> 2024-12-06T21:39:51 reactome_pathway-reactome_reaction
+> 2024-12-16T16:27:57 reactome_pathway-reactome_reaction
Rule for TSV (output/tsv/reactome_pathway-reactome_reaction.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-reactome_reaction.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:51 +0900
+timestamp: 2024-12-16 16:27:57 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:51 +0900)
-latest-prerequisite time: 2024-12-06 21:39:51 +0900
+--prepare:reactome (2024-12-16 16:27:57 +0900)
+latest-prerequisite time: 2024-12-16 16:27:57 +0900
................................
### Update TSV for reactome_pathway-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.7662957567867945 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:51 reactome_pathway-uniprot
+< 2024-12-16T16:27:57 reactome_pathway-uniprot
togoid-config config/reactome_pathway-uniprot update
# Success: output/tsv/reactome_pathway-uniprot.tsv is updated
-> 2024-12-06T21:39:53 reactome_pathway-uniprot
+> 2024-12-16T16:27:58 reactome_pathway-uniprot
Rule for TSV (output/tsv/reactome_pathway-uniprot.tsv)
------------------------------
Investigating output/tsv/reactome_pathway-uniprot.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:53 +0900
+timestamp: 2024-12-16 16:27:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:53 +0900)
-latest-prerequisite time: 2024-12-06 21:39:53 +0900
+--prepare:reactome (2024-12-16 16:27:58 +0900)
+latest-prerequisite time: 2024-12-16 16:27:58 +0900
................................
### Update TSV for reactome_reaction-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766299332748448 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:53 reactome_reaction-chebi
+< 2024-12-16T16:27:58 reactome_reaction-chebi
togoid-config config/reactome_reaction-chebi update
# Success: output/tsv/reactome_reaction-chebi.tsv is updated
-> 2024-12-06T21:39:53 reactome_reaction-chebi
+> 2024-12-16T16:27:59 reactome_reaction-chebi
Rule for TSV (output/tsv/reactome_reaction-chebi.tsv)
------------------------------
Investigating output/tsv/reactome_reaction-chebi.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:53 +0900
+timestamp: 2024-12-16 16:27:59 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:53 +0900)
-latest-prerequisite time: 2024-12-06 21:39:53 +0900
+--prepare:reactome (2024-12-16 16:27:59 +0900)
+latest-prerequisite time: 2024-12-16 16:27:59 +0900
................................
### Update TSV for reactome_reaction-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766299614092338 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:53 reactome_reaction-go
+< 2024-12-16T16:27:59 reactome_reaction-go
togoid-config config/reactome_reaction-go update
# Success: output/tsv/reactome_reaction-go.tsv is updated
-> 2024-12-06T21:39:53 reactome_reaction-go
+> 2024-12-16T16:27:59 reactome_reaction-go
Rule for TSV (output/tsv/reactome_reaction-go.tsv)
------------------------------
Investigating output/tsv/reactome_reaction-go.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:53 +0900
+timestamp: 2024-12-16 16:27:59 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:53 +0900)
-latest-prerequisite time: 2024-12-06 21:39:53 +0900
+--prepare:reactome (2024-12-16 16:27:59 +0900)
+latest-prerequisite time: 2024-12-16 16:27:59 +0900
................................
### Update TSV for reactome_reaction-iuphar_ligand if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766301614008923 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:53 reactome_reaction-iuphar_ligand
+< 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
-> 2024-12-06T21:39:54 reactome_reaction-iuphar_ligand
+> 2024-12-16T16:28:00 reactome_reaction-iuphar_ligand
Rule for TSV (output/tsv/reactome_reaction-iuphar_ligand.tsv)
------------------------------
Investigating output/tsv/reactome_reaction-iuphar_ligand.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:54 +0900
+timestamp: 2024-12-16 16:28:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:54 +0900)
-latest-prerequisite time: 2024-12-06 21:39:54 +0900
+--prepare:reactome (2024-12-16 16:28:00 +0900)
+latest-prerequisite time: 2024-12-16 16:28:00 +0900
................................
### Update TSV for reactome_reaction-mirbase if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766302377843125 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:54 reactome_reaction-mirbase
+< 2024-12-16T16:28:00 reactome_reaction-mirbase
togoid-config config/reactome_reaction-mirbase update
# Success: output/tsv/reactome_reaction-mirbase.tsv is updated
-> 2024-12-06T21:39:54 reactome_reaction-mirbase
+> 2024-12-16T16:28:00 reactome_reaction-mirbase
Rule for TSV (output/tsv/reactome_reaction-mirbase.tsv)
------------------------------
Investigating output/tsv/reactome_reaction-mirbase.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:54 +0900
+timestamp: 2024-12-16 16:28:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:54 +0900)
-latest-prerequisite time: 2024-12-06 21:39:54 +0900
+--prepare:reactome (2024-12-16 16:28:00 +0900)
+latest-prerequisite time: 2024-12-16 16:28:00 +0900
................................
### Update TSV for reactome_reaction-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766292733647418 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:39:54 reactome_reaction-uniprot
+< 2024-12-16T16:28:00 reactome_reaction-uniprot
togoid-config config/reactome_reaction-uniprot update
# Success: output/tsv/reactome_reaction-uniprot.tsv is updated
-> 2024-12-06T21:39:55 reactome_reaction-uniprot
+> 2024-12-16T16:28:01 reactome_reaction-uniprot
Rule for TSV (output/tsv/reactome_reaction-uniprot.tsv)
------------------------------
Investigating output/tsv/reactome_reaction-uniprot.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:39:55 +0900
+timestamp: 2024-12-16 16:28:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:reactome (2024-12-06 21:39:55 +0900)
-latest-prerequisite time: 2024-12-06 21:39:55 +0900
+--prepare:reactome (2024-12-16 16:28:01 +0900)
+latest-prerequisite time: 2024-12-16 16:28:01 +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
-< 2024-12-06T21:39:55 refseq_protein-uniprot
+< 2024-12-16T16:28:01 refseq_protein-uniprot
togoid-config config/refseq_protein-uniprot update
# Success: output/tsv/refseq_protein-uniprot.tsv is updated
-> 2024-12-06T21:46:09 refseq_protein-uniprot
+> 2024-12-16T16:35:33 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: 2024-12-06 21:46:09 +0900
+timestamp: 2024-12-16 16:35:33 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_protein (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_protein (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4326,8 +4214,8 @@ task needed: true
timestamp: 2024-11-16 05:24:22 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4342,8 +4230,8 @@ task needed: true
timestamp: 2024-11-16 05:27:15 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4358,8 +4246,8 @@ task needed: true
timestamp: 2024-11-16 05:31:03 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4374,8 +4262,8 @@ task needed: true
timestamp: 2024-11-16 05:32:50 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4390,8 +4278,8 @@ task needed: true
timestamp: 2024-11-16 05:34:56 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4406,8 +4294,8 @@ task needed: true
timestamp: 2024-11-16 05:38:35 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for refseq_rna-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4422,8 +4310,8 @@ task needed: true
timestamp: 2024-11-16 05:41:38 +0900
pre-requisites:
--output/tsv/ ()
---prepare:refseq_rna (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:refseq_rna (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-chebi if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4438,8 +4326,8 @@ task needed: true
timestamp: 2024-11-30 03:21:57 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4454,8 +4342,8 @@ task needed: true
timestamp: 2024-11-30 03:21:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4470,8 +4358,8 @@ task needed: true
timestamp: 2024-11-30 03:21:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4486,8 +4374,8 @@ task needed: true
timestamp: 2024-11-30 03:21:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-reactome_reaction if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4502,8 +4390,8 @@ task needed: true
timestamp: 2024-11-30 03:21:59 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for rhea-uniprot if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -4518,681 +4406,656 @@ task needed: true
timestamp: 2024-11-30 03:22:39 +0900
pre-requisites:
--output/tsv/ ()
---prepare:rhea (2024-12-06 21:46:09 +0900)
-latest-prerequisite time: 2024-12-06 21:46:09 +0900
+--prepare:rhea (2024-12-16 16:35:33 +0900)
+latest-prerequisite time: 2024-12-16 16:35:33 +0900
................................
### Update TSV for sra_accession-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764518614600811 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:46:09 sra_accession-bioproject
+< 2024-12-16T16:35:33 sra_accession-bioproject
togoid-config config/sra_accession-bioproject update
# Success: output/tsv/sra_accession-bioproject.tsv is updated
-> 2024-12-06T21:48:15 sra_accession-bioproject
+> 2024-12-16T16:36:55 sra_accession-bioproject
Rule for TSV (output/tsv/sra_accession-bioproject.tsv)
------------------------------
Investigating output/tsv/sra_accession-bioproject.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:48:15 +0900
+timestamp: 2024-12-16 16:36:55 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 21:48:15 +0900)
-latest-prerequisite time: 2024-12-06 21:48:15 +0900
+--prepare:sra (2024-12-16 16:36:55 +0900)
+latest-prerequisite time: 2024-12-16 16:36:55 +0900
................................
### Update TSV for sra_accession-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.760135071478125 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:48:15 sra_accession-biosample
+< 2024-12-16T16:36:55 sra_accession-biosample
togoid-config config/sra_accession-biosample update
# Success: output/tsv/sra_accession-biosample.tsv is updated
-> 2024-12-06T21:56:43 sra_accession-biosample
+> 2024-12-16T16:45:25 sra_accession-biosample
Rule for TSV (output/tsv/sra_accession-biosample.tsv)
------------------------------
Investigating output/tsv/sra_accession-biosample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:56:43 +0900
+timestamp: 2024-12-16 16:45:25 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 21:56:43 +0900)
-latest-prerequisite time: 2024-12-06 21:56:43 +0900
+--prepare:sra (2024-12-16 16:45:25 +0900)
+latest-prerequisite time: 2024-12-16 16:45:25 +0900
................................
### Update TSV for sra_accession-sra_analysis if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765207376045058 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:56:43 sra_accession-sra_analysis
+< 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
-> 2024-12-06T21:57:53 sra_accession-sra_analysis
+> 2024-12-16T16:46:35 sra_accession-sra_analysis
Rule for TSV (output/tsv/sra_accession-sra_analysis.tsv)
------------------------------
Investigating output/tsv/sra_accession-sra_analysis.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 21:57:53 +0900
+timestamp: 2024-12-16 16:46:35 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 21:57:53 +0900)
-latest-prerequisite time: 2024-12-06 21:57:53 +0900
+--prepare:sra (2024-12-16 16:46:35 +0900)
+latest-prerequisite time: 2024-12-16 16:46:35 +0900
................................
### Update TSV for sra_accession-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.761175293070232 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T21:57:53 sra_accession-sra_experiment
+< 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
-> 2024-12-06T22:04:51 sra_accession-sra_experiment
+> 2024-12-16T16:53:42 sra_accession-sra_experiment
Rule for TSV (output/tsv/sra_accession-sra_experiment.tsv)
------------------------------
Investigating output/tsv/sra_accession-sra_experiment.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:04:51 +0900
+timestamp: 2024-12-16 16:53:42 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:04:51 +0900)
-latest-prerequisite time: 2024-12-06 22:04:51 +0900
+--prepare:sra (2024-12-16 16:53:42 +0900)
+latest-prerequisite time: 2024-12-16 16:53:42 +0900
................................
### Update TSV for sra_accession-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765185197251019 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:04:51 sra_accession-sra_project
+< 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
-> 2024-12-06T22:06:00 sra_accession-sra_project
+> 2024-12-16T16:54:52 sra_accession-sra_project
Rule for TSV (output/tsv/sra_accession-sra_project.tsv)
------------------------------
Investigating output/tsv/sra_accession-sra_project.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:06:00 +0900
+timestamp: 2024-12-16 16:54:52 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:06:00 +0900)
-latest-prerequisite time: 2024-12-06 22:06:00 +0900
+--prepare:sra (2024-12-16 16:54:52 +0900)
+latest-prerequisite time: 2024-12-16 16:54:52 +0900
................................
### Update TSV for sra_accession-sra_run if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.760477615310185 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:06:00 sra_accession-sra_run
+< 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
-> 2024-12-06T22:14:07 sra_accession-sra_run
+> 2024-12-16T17:02:48 sra_accession-sra_run
Rule for TSV (output/tsv/sra_accession-sra_run.tsv)
------------------------------
Investigating output/tsv/sra_accession-sra_run.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:14:07 +0900
+timestamp: 2024-12-16 17:02:48 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:14:07 +0900)
-latest-prerequisite time: 2024-12-06 22:14:07 +0900
+--prepare:sra (2024-12-16 17:02:48 +0900)
+latest-prerequisite time: 2024-12-16 17:02:48 +0900
................................
### Update TSV for sra_accession-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.761450552270105 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:14:07 sra_accession-sra_sample
+< 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
-> 2024-12-06T22:20:59 sra_accession-sra_sample
+> 2024-12-16T17:09:41 sra_accession-sra_sample
Rule for TSV (output/tsv/sra_accession-sra_sample.tsv)
------------------------------
Investigating output/tsv/sra_accession-sra_sample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:20:59 +0900
+timestamp: 2024-12-16 17:09:41 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:20:59 +0900)
-latest-prerequisite time: 2024-12-06 22:20:59 +0900
+--prepare:sra (2024-12-16 17:09:41 +0900)
+latest-prerequisite time: 2024-12-16 17:09:41 +0900
................................
### Update TSV for sra_experiment-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763679812207835 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:20:59 sra_experiment-bioproject
+< 2024-12-16T17:09:41 sra_experiment-bioproject
togoid-config config/sra_experiment-bioproject update
# Success: output/tsv/sra_experiment-bioproject.tsv is updated
-> 2024-12-06T22:24:40 sra_experiment-bioproject
+> 2024-12-16T17:13:23 sra_experiment-bioproject
Rule for TSV (output/tsv/sra_experiment-bioproject.tsv)
------------------------------
Investigating output/tsv/sra_experiment-bioproject.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:24:40 +0900
+timestamp: 2024-12-16 17:13:23 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:24:40 +0900)
-latest-prerequisite time: 2024-12-06 22:24:40 +0900
+--prepare:sra (2024-12-16 17:13:23 +0900)
+latest-prerequisite time: 2024-12-16 17:13:23 +0900
................................
### Update TSV for sra_experiment-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763762468424502 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:24:40 sra_experiment-biosample
+< 2024-12-16T17:13:23 sra_experiment-biosample
togoid-config config/sra_experiment-biosample update
# Success: output/tsv/sra_experiment-biosample.tsv is updated
-> 2024-12-06T22:28:12 sra_experiment-biosample
+> 2024-12-16T17:16:58 sra_experiment-biosample
Rule for TSV (output/tsv/sra_experiment-biosample.tsv)
------------------------------
Investigating output/tsv/sra_experiment-biosample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:28:12 +0900
+timestamp: 2024-12-16 17:16:58 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:28:12 +0900)
-latest-prerequisite time: 2024-12-06 22:28:12 +0900
+--prepare:sra (2024-12-16 17:16:58 +0900)
+latest-prerequisite time: 2024-12-16 17:16:58 +0900
................................
### Update TSV for sra_experiment-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764102618669641 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:28:12 sra_experiment-sra_project
+< 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
-> 2024-12-06T22:31:15 sra_experiment-sra_project
+> 2024-12-16T17:20:02 sra_experiment-sra_project
Rule for TSV (output/tsv/sra_experiment-sra_project.tsv)
------------------------------
Investigating output/tsv/sra_experiment-sra_project.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:31:15 +0900
+timestamp: 2024-12-16 17:20:02 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:31:15 +0900)
-latest-prerequisite time: 2024-12-06 22:31:15 +0900
+--prepare:sra (2024-12-16 17:20:02 +0900)
+latest-prerequisite time: 2024-12-16 17:20:02 +0900
................................
### Update TSV for sra_experiment-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764148830157802 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:31:15 sra_experiment-sra_sample
+< 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
-> 2024-12-06T22:34:12 sra_experiment-sra_sample
+> 2024-12-16T17:23:00 sra_experiment-sra_sample
Rule for TSV (output/tsv/sra_experiment-sra_sample.tsv)
------------------------------
Investigating output/tsv/sra_experiment-sra_sample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:34:12 +0900
+timestamp: 2024-12-16 17:23:00 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:34:12 +0900)
-latest-prerequisite time: 2024-12-06 22:34:12 +0900
+--prepare:sra (2024-12-16 17:23:00 +0900)
+latest-prerequisite time: 2024-12-16 17:23:00 +0900
................................
### Update TSV for sra_project-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765391987098611 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:34:12 sra_project-bioproject
+< 2024-12-16T17:23:00 sra_project-bioproject
togoid-config config/sra_project-bioproject update
# Success: output/tsv/sra_project-bioproject.tsv is updated
-> 2024-12-06T22:35:23 sra_project-bioproject
+> 2024-12-16T17:24:09 sra_project-bioproject
Rule for TSV (output/tsv/sra_project-bioproject.tsv)
------------------------------
Investigating output/tsv/sra_project-bioproject.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:35:23 +0900
+timestamp: 2024-12-16 17:24:09 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:35:23 +0900)
-latest-prerequisite time: 2024-12-06 22:35:23 +0900
+--prepare:sra (2024-12-16 17:24:09 +0900)
+latest-prerequisite time: 2024-12-16 17:24:09 +0900
................................
### Update TSV for sra_run-bioproject if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763349539270278 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:35:23 sra_run-bioproject
+< 2024-12-16T17:24:09 sra_run-bioproject
togoid-config config/sra_run-bioproject update
# Success: output/tsv/sra_run-bioproject.tsv is updated
-> 2024-12-06T22:39:29 sra_run-bioproject
+> 2024-12-16T17:28:18 sra_run-bioproject
Rule for TSV (output/tsv/sra_run-bioproject.tsv)
------------------------------
Investigating output/tsv/sra_run-bioproject.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:39:29 +0900
+timestamp: 2024-12-16 17:28:18 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:39:29 +0900)
-latest-prerequisite time: 2024-12-06 22:39:29 +0900
+--prepare:sra (2024-12-16 17:28:18 +0900)
+latest-prerequisite time: 2024-12-16 17:28:18 +0900
................................
### Update TSV for sra_run-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763428903616817 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:39:29 sra_run-biosample
+< 2024-12-16T17:28:18 sra_run-biosample
togoid-config config/sra_run-biosample update
# Success: output/tsv/sra_run-biosample.tsv is updated
-> 2024-12-06T22:43:32 sra_run-biosample
+> 2024-12-16T17:32:19 sra_run-biosample
Rule for TSV (output/tsv/sra_run-biosample.tsv)
------------------------------
Investigating output/tsv/sra_run-biosample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:43:32 +0900
+timestamp: 2024-12-16 17:32:19 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:43:32 +0900)
-latest-prerequisite time: 2024-12-06 22:43:32 +0900
+--prepare:sra (2024-12-16 17:32:19 +0900)
+latest-prerequisite time: 2024-12-16 17:32:19 +0900
................................
### Update TSV for sra_run-sra_experiment if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764081250621528 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:43:32 sra_run-sra_experiment
+< 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
-> 2024-12-06T22:46:38 sra_run-sra_experiment
+> 2024-12-16T17:35:30 sra_run-sra_experiment
Rule for TSV (output/tsv/sra_run-sra_experiment.tsv)
------------------------------
Investigating output/tsv/sra_run-sra_experiment.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:46:38 +0900
+timestamp: 2024-12-16 17:35:30 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:46:38 +0900)
-latest-prerequisite time: 2024-12-06 22:46:38 +0900
+--prepare:sra (2024-12-16 17:35:30 +0900)
+latest-prerequisite time: 2024-12-16 17:35:30 +0900
................................
### Update TSV for sra_run-sra_project if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763877522089421 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:46:38 sra_run-sra_project
+< 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
-> 2024-12-06T22:49:59 sra_run-sra_project
+> 2024-12-16T17:38:52 sra_run-sra_project
Rule for TSV (output/tsv/sra_run-sra_project.tsv)
------------------------------
Investigating output/tsv/sra_run-sra_project.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:49:59 +0900
+timestamp: 2024-12-16 17:38:52 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:49:59 +0900)
-latest-prerequisite time: 2024-12-06 22:49:59 +0900
+--prepare:sra (2024-12-16 17:38:52 +0900)
+latest-prerequisite time: 2024-12-16 17:38:52 +0900
................................
### Update TSV for sra_run-sra_sample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763951409057964 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:49:59 sra_run-sra_sample
+< 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
-> 2024-12-06T22:53:13 sra_run-sra_sample
+> 2024-12-16T17:42:11 sra_run-sra_sample
Rule for TSV (output/tsv/sra_run-sra_sample.tsv)
------------------------------
Investigating output/tsv/sra_run-sra_sample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:53:13 +0900
+timestamp: 2024-12-16 17:42:10 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:53:13 +0900)
-latest-prerequisite time: 2024-12-06 22:53:13 +0900
+--prepare:sra (2024-12-16 17:42:11 +0900)
+latest-prerequisite time: 2024-12-16 17:42:11 +0900
................................
### Update TSV for sra_sample-biosample if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763966360204873 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:53:13 sra_sample-biosample
+< 2024-12-16T17:42:11 sra_sample-biosample
togoid-config config/sra_sample-biosample update
# Success: output/tsv/sra_sample-biosample.tsv is updated
-> 2024-12-06T22:56:25 sra_sample-biosample
+> 2024-12-16T17:45:26 sra_sample-biosample
Rule for TSV (output/tsv/sra_sample-biosample.tsv)
------------------------------
Investigating output/tsv/sra_sample-biosample.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:56:25 +0900
+timestamp: 2024-12-16 17:45:26 +0900
pre-requisites:
--output/tsv/ ()
---prepare:sra (2024-12-06 22:56:25 +0900)
-latest-prerequisite time: 2024-12-06 22:56:25 +0900
+--prepare:sra (2024-12-16 17:45:26 +0900)
+latest-prerequisite time: 2024-12-16 17:45:26 +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
-< 2024-12-06T22:56:25 swisslipids-chebi
+< 2024-12-16T17:45:26 swisslipids-chebi
togoid-config config/swisslipids-chebi update
# Success: output/tsv/swisslipids-chebi.tsv is updated
-> 2024-12-06T22:56:39 swisslipids-chebi
+> 2024-12-16T17:45:40 swisslipids-chebi
Rule for TSV (output/tsv/swisslipids-chebi.tsv)
------------------------------
Investigating output/tsv/swisslipids-chebi.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:56:39 +0900
+timestamp: 2024-12-16 17:45:40 +0900
pre-requisites:
--output/tsv/ ()
---prepare:swisslipids (2024-12-06 22:56:39 +0900)
-latest-prerequisite time: 2024-12-06 22:56:39 +0900
+--prepare:swisslipids (2024-12-16 17:45:40 +0900)
+latest-prerequisite time: 2024-12-16 17:45:40 +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
-< 2024-12-06T22:56:39 swisslipids-hmdb
+< 2024-12-16T17:45:40 swisslipids-hmdb
togoid-config config/swisslipids-hmdb update
# Success: output/tsv/swisslipids-hmdb.tsv is updated
-> 2024-12-06T22:56:53 swisslipids-hmdb
+> 2024-12-16T17:45:53 swisslipids-hmdb
Rule for TSV (output/tsv/swisslipids-hmdb.tsv)
------------------------------
Investigating output/tsv/swisslipids-hmdb.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:56:53 +0900
+timestamp: 2024-12-16 17:45:53 +0900
pre-requisites:
--output/tsv/ ()
---prepare:swisslipids (2024-12-06 22:56:53 +0900)
-latest-prerequisite time: 2024-12-06 22:56:53 +0900
+--prepare:swisslipids (2024-12-16 17:45:53 +0900)
+latest-prerequisite time: 2024-12-16 17:45:53 +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
-< 2024-12-06T22:56:53 swisslipids-inchi_key
+< 2024-12-16T17:45:53 swisslipids-inchi_key
togoid-config config/swisslipids-inchi_key update
# Success: output/tsv/swisslipids-inchi_key.tsv is updated
-> 2024-12-06T22:57:05 swisslipids-inchi_key
+> 2024-12-16T17:46:06 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: 2024-12-06 22:57:05 +0900
+timestamp: 2024-12-16 17:46:06 +0900
pre-requisites:
--output/tsv/ ()
---prepare:swisslipids (2024-12-06 22:57:05 +0900)
-latest-prerequisite time: 2024-12-06 22:57:05 +0900
+--prepare:swisslipids (2024-12-16 17:46:06 +0900)
+latest-prerequisite time: 2024-12-16 17:46:06 +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
-< 2024-12-06T22:57:05 taxonomy-pubmed
+< 2024-12-16T17:46:06 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
-> 2024-12-06T22:57:06 taxonomy-pubmed
+> 2024-12-16T17:46:06 taxonomy-pubmed
Rule for TSV (output/tsv/taxonomy-pubmed.tsv)
------------------------------
Investigating output/tsv/taxonomy-pubmed.tsv
class: Rake::FileTask
task needed: true
-timestamp: 2024-12-06 22:57:06 +0900
+timestamp: 2024-12-16 17:46:06 +0900
pre-requisites:
--output/tsv/ ()
---prepare:taxonomy (2024-12-06 22:57:06 +0900)
-latest-prerequisite time: 2024-12-06 22:57:06 +0900
+--prepare:taxonomy (2024-12-16 17:46:06 +0900)
+latest-prerequisite time: 2024-12-16 17:46:06 +0900
................................
### Update TSV for togovar-clinvar if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765525226906435 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:57:06 togovar-clinvar
+< 2024-12-16T17:46:06 togovar-clinvar
togoid-config config/togovar-clinvar update
# Success: output/tsv/togovar-clinvar.tsv is updated
-> 2024-12-06T22:58:22 togovar-clinvar
+> 2024-12-16T17:47:06 togovar-clinvar
Rule for TSV (output/tsv/togovar-clinvar.tsv)
------------------------------
Investigating output/tsv/togovar-clinvar.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 22:58:22 +0900
+timestamp: 2024-12-16 17:47:06 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.766010506814015 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:58:22 togovar-dbsnp
+< 2024-12-16T17:47:06 togovar-dbsnp
togoid-config config/togovar-dbsnp update
# Success: output/tsv/togovar-dbsnp.tsv is updated
-> 2024-12-06T22:58:56 togovar-dbsnp
+> 2024-12-16T17:47:41 togovar-dbsnp
Rule for TSV (output/tsv/togovar-dbsnp.tsv)
------------------------------
Investigating output/tsv/togovar-dbsnp.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 22:58:56 +0900
+timestamp: 2024-12-16 17:47:41 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.765957181273484 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:58:56 togovar-ensembl_gene
+< 2024-12-16T17:47:41 togovar-ensembl_gene
togoid-config config/togovar-ensembl_gene update
# Success: output/tsv/togovar-ensembl_gene.tsv is updated
-> 2024-12-06T22:59:36 togovar-ensembl_gene
+> 2024-12-16T17:48:22 togovar-ensembl_gene
Rule for TSV (output/tsv/togovar-ensembl_gene.tsv)
------------------------------
Investigating output/tsv/togovar-ensembl_gene.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 22:59:36 +0900
+timestamp: 2024-12-16 17:48:22 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764731694658704 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:59:36 togovar-ensembl_transcript
+< 2024-12-16T17:48:22 togovar-ensembl_transcript
togoid-config config/togovar-ensembl_transcript update
-# Error: output/tsv/togovar-ensembl_transcript.tsv new file size per old 0 / 8069270901 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-ensembl_transcript.tsv or created file was empty
-# Failure: output/tsv/togovar-ensembl_transcript.tsv is not updated
-> 2024-12-06T22:59:36 togovar-ensembl_transcript
+# Success: output/tsv/togovar-ensembl_transcript.tsv is updated
+> 2024-12-16T17:50:47 togovar-ensembl_transcript
Rule for TSV (output/tsv/togovar-ensembl_transcript.tsv)
------------------------------
Investigating output/tsv/togovar-ensembl_transcript.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 04:38:23 +0900
+task needed: false
+timestamp: 2024-12-16 17:50:47 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764433290915231 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T22:59:36 togovar-hgnc
+< 2024-12-16T17:50:47 togovar-hgnc
togoid-config config/togovar-hgnc update
# Success: output/tsv/togovar-hgnc.tsv is updated
-> 2024-12-06T23:00:00 togovar-hgnc
+> 2024-12-16T17:51:10 togovar-hgnc
Rule for TSV (output/tsv/togovar-hgnc.tsv)
------------------------------
Investigating output/tsv/togovar-hgnc.tsv
class: Rake::FileTask
task needed: false
-timestamp: 2024-12-06 23:00:00 +0900
+timestamp: 2024-12-16 17:51:10 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764445991901805 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T23:00:00 togovar-ncbigene
+< 2024-12-16T17:51:10 togovar-ncbigene
togoid-config config/togovar-ncbigene update
-# Error: output/tsv/togovar-ncbigene.tsv new file size per old 0 / 1097267175 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-ncbigene.tsv or created file was empty
-# Failure: output/tsv/togovar-ncbigene.tsv is not updated
-> 2024-12-06T23:00:00 togovar-ncbigene
+# Success: output/tsv/togovar-ncbigene.tsv is updated
+> 2024-12-16T17:51:33 togovar-ncbigene
Rule for TSV (output/tsv/togovar-ncbigene.tsv)
------------------------------
Investigating output/tsv/togovar-ncbigene.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 04:39:12 +0900
+task needed: false
+timestamp: 2024-12-16 17:51:33 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-pubmed if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.764441307595567 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T23:00:00 togovar-pubmed
+< 2024-12-16T17:51:33 togovar-pubmed
togoid-config config/togovar-pubmed update
-# Error: output/tsv/togovar-pubmed.tsv new file size per old 0 / 14408635 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-pubmed.tsv or created file was empty
-# Failure: output/tsv/togovar-pubmed.tsv is not updated
-> 2024-12-06T23:00:01 togovar-pubmed
+# Success: output/tsv/togovar-pubmed.tsv is updated
+> 2024-12-16T17:51:34 togovar-pubmed
Rule for TSV (output/tsv/togovar-pubmed.tsv)
------------------------------
Investigating output/tsv/togovar-pubmed.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 04:39:13 +0900
+task needed: false
+timestamp: 2024-12-16 17:51:34 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for togovar-refseq_rna if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763481022798577 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T23:00:01 togovar-refseq_rna
+< 2024-12-16T17:51:34 togovar-refseq_rna
togoid-config config/togovar-refseq_rna update
-# Error: output/tsv/togovar-refseq_rna.tsv new file size per old 0 / 4180808277 = 0.0 < 0.5
-# Error: Failed to create output/tsv/togovar-refseq_rna.tsv or created file was empty
-# Failure: output/tsv/togovar-refseq_rna.tsv is not updated
-> 2024-12-06T23:00:01 togovar-refseq_rna
+# Success: output/tsv/togovar-refseq_rna.tsv is updated
+> 2024-12-16T17:53:04 togovar-refseq_rna
Rule for TSV (output/tsv/togovar-refseq_rna.tsv)
------------------------------
Investigating output/tsv/togovar-refseq_rna.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 04:40:36 +0900
+task needed: false
+timestamp: 2024-12-16 17:53:04 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for uberon-ncit_tissue if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp true
# 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 6.763462701142522 days ago (will be updated when >5 days)
+# 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
-< 2024-12-06T23:00:01 uberon-ncit_tissue
+< 2024-12-16T17:53:04 uberon-ncit_tissue
togoid-config config/uberon-ncit_tissue update
-# Error: output/tsv/uberon-ncit_tissue.tsv new file size per old 288 / 38722 = 0.007437632353700738 < 0.5
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML 502 Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server received an invalid
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request
Reason: Error reading from remote server
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML 502 Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML Proxy Error
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server received an invalid
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request
Reason: Error reading from remote server
-# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML
-# Failure: output/tsv/uberon-ncit_tissue.tsv is not updated
-> 2024-12-06T23:02:14 uberon-ncit_tissue
+# Success: output/tsv/uberon-ncit_tissue.tsv is updated
+> 2024-12-16T17:53:05 uberon-ncit_tissue
Rule for TSV (output/tsv/uberon-ncit_tissue.tsv)
------------------------------
Investigating output/tsv/uberon-ncit_tissue.tsv
class: Rake::FileTask
-task needed: true
-timestamp: 2024-11-30 04:40:38 +0900
+task needed: false
+timestamp: 2024-12-16 17:53:05 +0900
pre-requisites:
--output/tsv/ ()
---input/update.txt (2024-12-06 19:52:55 +0900)
-latest-prerequisite time: 2024-12-06 19:52:55 +0900
+--input/update.txt (2024-12-16 01:06:15 +0900)
+latest-prerequisite time: 2024-12-16 01:06:15 +0900
................................
### Update TSV for uniprot-chembl_target if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5207,8 +5070,8 @@ task needed: true
timestamp: 2024-11-30 05:19:45 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-dbsnp if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5223,8 +5086,8 @@ task needed: true
timestamp: 2024-11-30 05:20:10 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-ec if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5239,8 +5102,8 @@ task needed: true
timestamp: 2024-11-30 05:55:03 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-ensembl_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5255,8 +5118,8 @@ task needed: true
timestamp: 2024-11-30 06:42:45 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-ensembl_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5271,8 +5134,8 @@ task needed: true
timestamp: 2024-11-30 07:29:45 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-ensembl_transcript if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5287,8 +5150,8 @@ task needed: true
timestamp: 2024-11-30 08:16:54 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-go if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5303,8 +5166,8 @@ task needed: true
timestamp: 2024-11-30 08:36:07 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-hgnc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5319,8 +5182,8 @@ task needed: true
timestamp: 2024-11-30 09:14:30 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-insdc if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5335,8 +5198,8 @@ task needed: true
timestamp: 2024-11-30 10:00:39 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-intact if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5351,8 +5214,8 @@ task needed: true
timestamp: 2024-11-30 10:02:02 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-ncbigene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5367,8 +5230,8 @@ task needed: true
timestamp: 2024-11-30 10:41:09 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-oma_group if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5383,8 +5246,8 @@ task needed: true
timestamp: 2024-11-30 11:20:53 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-omim_gene if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5399,8 +5262,8 @@ task needed: true
timestamp: 2024-11-30 11:21:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-omim_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5415,8 +5278,8 @@ task needed: true
timestamp: 2024-11-30 11:21:04 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-orphanet_phenotype if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5431,8 +5294,8 @@ task needed: true
timestamp: 2024-11-30 12:07:53 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-pdb if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5447,8 +5310,8 @@ task needed: true
timestamp: 2024-11-30 12:47:53 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-reactome_pathway if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5463,8 +5326,8 @@ task needed: true
timestamp: 2024-11-30 13:34:50 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-refseq_protein if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5479,8 +5342,8 @@ task needed: true
timestamp: 2024-11-30 14:15:09 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-taxonomy if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5495,8 +5358,8 @@ task needed: true
timestamp: 2024-11-30 14:50:01 +0900
pre-requisites:
--output/tsv/ ()
---prepare:uniprot (2024-12-06 23:02:14 +0900)
-latest-prerequisite time: 2024-12-06 23:02:14 +0900
+--prepare:uniprot (2024-12-16 17:53:06 +0900)
+latest-prerequisite time: 2024-12-16 17:53:06 +0900
................................
### Update TSV for uniprot-uniprot_mnemonic if check_tsv_filesize false or check_config_timestamp false or check_tsv_timestamp false
@@ -5511,182 +5374,188 @@ task needed: true
timestamp: 2024-11-30 15:46:15 +0900
pre-requisites:
--output/tsv/ (