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call_snp_RNA-seq.err
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Config file config.yaml is extended by additional config specified via the command line.
Config file config.yaml is extended by additional config specified via the command line.
Config file config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Building DAG of jobs...
Using shell: /usr/bin/bash
Using shell: /usr/bin/bash
Using shell: /usr/bin/bash
Provided cores: 8
Provided cores: 8
Provided cores: 8
Rules claiming more threads will be scaled down.
Rules claiming more threads will be scaled down.
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=10428, mem_mib=9945, disk_mb=10428, disk_mib=9945
Provided resources: mem_mb=10000, mem_mib=9537, disk_mb=10290, disk_mib=9814
Provided resources: mem_mb=10000, mem_mib=9537, disk_mb=13501, disk_mib=12876
Select jobs to execute...
Select jobs to execute...
Select jobs to execute...
[Mon Nov 6 04:21:43 2023]
[Mon Nov 6 04:21:43 2023]
rule fastqc:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-86/Sample_3266-CB-86.R1.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R1_fastqc.html, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R1_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-86, read=R1
resources: mem_mb=10000, mem_mib=9537, disk_mb=10290, disk_mib=9814, tmpdir=/tmp
rule fastqc:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-180/Sample_3266-CB-180.R2.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.html, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-180, read=R2
resources: mem_mb=10000, mem_mib=9537, disk_mb=13501, disk_mib=12876, tmpdir=/tmp
[Mon Nov 6 04:21:43 2023]
rule trimmomatic:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-95/Sample_3266-CB-95.R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-95/Sample_3266-CB-95.R2.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-95_R1_val_R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-95_R2_val_R2.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-95_1_unpai.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-95_2_unpai.fq.gz
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-95
resources: mem_mb=10428, mem_mib=9945, disk_mb=10428, disk_mib=9945, tmpdir=/tmp
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
TrimmomaticPE: Started with arguments:
-threads 1 -phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-95/Sample_3266-CB-95.R1.fq.gzApprox 40% complete for Sample_3266-CB-180.R2.fq.gz
phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-86/Sample_3266-CB-86.R1.fq.gz /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-86/Sample_3266-CB-86.R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-86_R1_val_R1.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-86_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-86_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-86_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
ces, 0 forward only sequences, 0 reverse only sequences
nformation please use:
$ module help Bioinformatics
Sample_3266-CB-200.R1.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R1_fastqc.html, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R1_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-200, read=R1
resources: mem_mb=10000, mem_mib=9537, disk_mb=8064, disk_mib=7691, tmpdir=/tmp
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
complete for Sample_3266-CB-77.R1.fq.gz
Approx 45% complete for Sample_3266-CB-237.R2.fq.gz
Approx 35% complete for Sample_3266-CB-77.R1.fq.gz
Approx 50% complete for Sample_3266-CB-237.R2.fq.gz
Approx 70% complete for Sample_3266-CB-65.R2.fq.gz
Approx 80% complete for Sample_3266-CB-65.R2.fq.gz
rted analysis of Sample_3266-CB-64.R2.fq.gz
Started analysis of Sample_3266-CB-86.R2.fq.gz
Started analysis of Sample_3266-CB-200.R1.fq.gz
Started analysis of Sample_3266-CB-96.R1.fq.gz
TrimmomaticPE: Started with arguments:
-threads 1 -phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-200/Sample_3266-CB-200.R1.fq.gz /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-200/Sample_3266-CB-200.R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-200_R1_val_R1.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-200_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-200_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-200_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
_files/Sample_3266-CB-63_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-63_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-63_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Started analysis of Sample_3266-CB-93.R2.fq.gz
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.html, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-180, read=R1
resources: mem_mb=10000, mem_mib=9537, disk_mb=13378, disk_mib=12759, tmpdir=/tmp
rule fastqc:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-206/Sample_3266-CB-206.R1.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R1_fastqc.html, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R1_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-206, read=R1
resources: mem_mb=10000, mem_mib=9537, disk_mb=9249, disk_mib=8821, tmpdir=/tmp
[Mon Nov 6 04:26:46 2023]
rule trimmomatic:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-85/Sample_3266-CB-85.R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-85/Sample_3266-CB-85.R2.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-85_R1_val_R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-85_R2_val_R2.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-85_1_unpai.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-85_2_unpai.fq.gz
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-85
resources: mem_mb=18784, mem_mib=17914, disk_mb=18784, disk_mib=17914, tmpdir=/tmp
Approx 50% complete for Sample_3266-CB-75.R2.fq.gz
-phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-107/Sample_3266-CB-107.R1.fq.gzTrimmomaticPE: Started with arguments: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-107/Sample_3266-CB-107.R2.fq.gz
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-107_R1_val_R1.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-107_1_unpai.fq.gz -threads /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-107_R2_val_R2.fq.gz 1 /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-107_2_unpai.fq.gz -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-98/Sample_3266-CB-98.R1.fq.gz LEADING:3 TRAILING:3 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-98/Sample_3266-CB-98.R2.fq.gz SLIDINGWINDOW:4:15 /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-98_R1_val_R1.fq.gz MINLEN:36
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-98_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-98_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-98_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Started analysis of Sample_3266-CB-107.R1.fq.gz
tml, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R2_fastqc.zip
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-200, read=R2
resources: mem_mb=10000, mem_mib=9537, disk_mb=8223, disk_mib=7843, tmpdir=/tmp
[Mon Nov 6 04:26:47 2023]
[Mon Nov 6 04:26:47 2023]
rule trimmomatic:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-237/Sample_3266-CB-237.R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-237/Sample_3266-CB-237.R2.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_R1_val_R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_R2_val_R2.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_1_unpai.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_2_unpai.fq.gz
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-237
resources: mem_mb=18083, mem_mib=17246, disk_mb=18083, disk_mib=17246, tmpdir=/tmp
rule trimmomatic:
input: /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-65/Sample_3266-CB-65.R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-65/Sample_3266-CB-65.R2.fq.gz
output: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_R1_val_R1.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_R2_val_R2.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_1_unpai.fq.gz, /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_2_unpai.fq.gz
jobid: 0
reason: Forced execution
wildcards: file=Sample_3266-CB-65
resources: mem_mb=14591, mem_mib=13916, disk_mb=14591, disk_mib=13916, tmpdir=/tmp
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
Provides Bioinformatics software.
For more information please use:
$ module help Bioinformatics
TrimmomaticPE: Started with arguments:
-threads 1 -phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-237/Sample_3266-CB-237.R1.fq.gz /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-237/Sample_3266-CB-237.R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_R1_val_R1.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-237_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36TrimmomaticPE: Started with arguments:
-threads 1 -phred33 /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-65/Sample_3266-CB-65.R1.fq.gz /home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP/Sample_3266-CB-65/Sample_3266-CB-65.R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_R1_val_R1.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_1_unpai.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_R2_val_R2.fq.gz /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/trimmed_files/Sample_3266-CB-65_2_unpai.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Started analysis of Sample_3266-CB-64.R1.fq.gzStarted analysis of Sample_3266-CB-200.R2.fq.gz
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Approx 5% complete for Sample_3266-CB-200.R2.fq.gz
Approx 5% complete for Sample_3266-CB-64.R1.fq.gz
Approx 10% complete for Sample_3266-CB-200.R2.fq.gz
Approx 10% complete for Sample_3266-CB-64.R1.fq.gz
Approx 15% complete for Sample_3266-CB-65.R2.fq.gz
Approx 20% complete for Sample_3266-CB-291.R2.fq.gz
Approx 20% complete for Sample_3266-CB-65.R2.fq.gz
Approx 25% complete for Sample_3266-CB-291.R2.fq.gz
Approx 25% complete for Sample_3266-CB-65.R2.fq.gz
Approx 30% complete for Sample_3266-CB-291.R2.fq.gz
Approx 30% complete for Sample_3266-CB-65.R2.fq.gz
Approx 75% complete for Sample_3266-CB-96.R1.fq.gz
Approx 25% complete for Sample_3266-CB-107.R2.fq.gz
Approx 35% complete for Sample_3266-CB-65.R2.fq.gz
Approx 35% complete for Sample_3266-CB-93.R1.fq.gz
Approx 85% complete for Sample_3266-CB-248.R2.fq.gz
es are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 55% complete for Sample_3266-CB-95.R1.fq.gz
aiting at most 60 seconds for missing files.
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 70% complete for Sample_3266-CB-77.R2.fq.gz
Approx 35% complete for Sample_3266-CB-200.R1.fq.gz
Approx 35% complete for Sample_3266-CB-200.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-291_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-291_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 25% complete for Sample_3266-CB-107.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-291_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-291_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 65% complete for Sample_3266-CB-98.R2.fq.gz
Approx 40% complete for Sample_3266-CB-291.R2.fq.gz
Approx 40% complete for Sample_3266-CB-90.R2.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 25% complete for Sample_3266-CB-57.R1.fq.gz
Approx 40% complete for Sample_3266-CB-80.R1.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 80% complete for Sample_3266-CB-64.R1.fq.gz
Waiting at most 60 seconds for missing files.
q.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-65_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-65_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-86.R2.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-85.R1.fq.gz
Approx 30% complete for Sample_3266-CB-96.R1.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 10% complete for Sample_3266-CB-107.R1.fq.gz
Approx 35% complete for Sample_3266-CB-85.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 25% complete for Sample_3266-CB-98.R2.fq.gz
pprox 70% complete for Sample_3266-CB-95.R2.fq.gz
NP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-206.R2.fq.gz
pprox 40% complete for Sample_3266-CB-282.R2.fq.gz
Approx 30% complete for Sample_3266-CB-77.R2.fq.gz
9:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 10% complete for Sample_3266-CB-107.R2.fq.gz
issingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-96.R1.fq.gz
Approx 95% complete for Sample_3266-CB-86.R1.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-237_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-237_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-64.R1.fq.gz
Approx 55% complete for Sample_3266-CB-90.R2.fq.gz
pprox 55% complete for Sample_3266-CB-90.R1.fq.gz
49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-282_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-282_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-86.R2.fq.gz
Approx 30% complete for Sample_3266-CB-180.R2.fq.gz
rbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-200_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 80% complete for Sample_3266-CB-57.R1.fq.gz
Waiting at most 60 seconds for missing files.
q.gz
Approx 60% complete for Sample_3266-CB-200.R1.fq.gz
Approx 45% complete for Sample_3266-CB-96.R1.fq.gz
9:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 15% complete for Sample_3266-CB-107.R1.fq.gz
Approx 85% complete for Sample_3266-CB-57.R2.fq.gz
Approx 70% complete for Sample_3266-CB-291.R2.fq.gz
_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
q.gz
Approx 70% complete for Sample_3266-CB-291.R1.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-237_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-237_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-77.R1.fq.gz
Approx 90% complete for Sample_3266-CB-77.R1.fq.gz
pprox 75% complete for Sample_3266-CB-200.R2.fq.gz
rbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-95_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-95_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 55% complete for Sample_3266-CB-75.R1.fq.gz
Approx 35% complete for Sample_3266-CB-107.R1.fq.gz
Approx 85% complete for Sample_3266-CB-90.R2.fq.gz
Approx 75% complete for Sample_3266-CB-282.R1.fq.gz
Approx 20% complete for Sample_3266-CB-107.R1.fq.gz
Approx 60% complete for Sample_3266-CB-64.R1.fq.gz
Approx 55% complete for Sample_3266-CB-57.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 65% complete for Sample_3266-CB-86.R1.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-207_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-207_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-77.R1.fq.gz
AApprox 70% complete for Sample_3266-CB-85.R2.fq.gz
pApprox 75% complete for Sample_3266-CB-206.R1.fq.gz
Approx 20% complete for Sample_3266-CB-107.R2.fq.gz
pprox 80% complete for Sample_3266-CB-237.R2.fq.gz
Approx 85% complete for Sample_3266-CB-282.R1.fq.gz
:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-200.R2.ApproApprox 75% complete for Sample_3266-CB-207.R2.fq.gz
pApprox 95% complete for Sample_3266-CB-180.R2.fq.gz
rox 95% complete for Sample_3266-CB-80.R2.fq.gz
Approx 55% complete for Sample_3266-CB-98.R2.fq.gz
Approx 55% complete for Sample_3266-CB-98.R1.fq.gz
NP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-237.R2.fq.gz
Approx 90% complete for Sample_3266-CB-282.R1.fq.gz
rse Only Surviving: 13222 (0.14%) Dropped: 48791 (0.51%)
TrimmomaticPE: Completed successfully
Approx 70% complete for Sample_3266-CB-64.R1.fq.gz
Approx 95% compleApprox 40% complete for Sample_3266-CB-107.R2.fq.gz
Approx 55% complete for Sample_3266-CB-180.R2.fq.gz
Approx 85% complete for Sample_3266-CB-206.R2.fq.gz
RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 70% complete for Sample_3266-CB-96.R2.fq.gz
Approx 25% complete for Sample_3266-CB-107.R1.fq.gz
75% complete for Sample_3266-CB-64.R1.fq.gz
Approx 70% complete for Sample_3266-CB-57.R1.fq.gz
Approx 75% complete for Sample_3266-CB-96.R2.fq.gz
Waiting at most 60 seconds for missing files.
Approx 80% complete for Sample_3266-CB-96.R1.fq.gz
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 75% complete for Sample_3266-CB-75.R2.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 80% complete for Sample_3266-CB-64.R1.fq.gz
Approx 75% complete for Sample_3266-CB-77.R1.fq.gz
P_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-90_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 25% complete for Sample_3266-CB-107.R2.fq.gz
pprox 95% complete for Sample_3266-CB-206.R1.fq.gz
gOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-80_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-207.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-93_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 80% complete for Sample_3266-CB-96.R2.fq.gz
Approx 75% complete for Sample_3266-CB-57.R1.fq.gz
Approx 80% complete for Sample_3266-CB-75.R2.fq.gz
Approx 80% complete for Sample_3266-CB-77.R2.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-63_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-86.R2.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
q.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 45% complete for Sample_3266-CB-107.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-75.R1.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 80% complete for Sample_3266-CB-57.R1.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-282_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-282_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 45% complete for Sample_3266-CB-107.R1.fq.gz
Approx 75% complete for Sample_3266-CB-57.R2.fq.gz
turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-292_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 70% complete for Sample_3266-CB-180.R2.fq.gz
Waiting at most 60 seconds for missing files.
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-64.R2.fq.gz
aiting at most 60 seconds for missing files.
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-206_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 95% complete for Sample_3266-CB-75.R2.fq.gz
g at most 60 seconds for missing files.
.R1.fq.gz
/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-85_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 50% complete for Sample_3266-CB-107.R1.fq.gz
95% complete for Sample_3266-CB-57.R1.fq.gz
all_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-207_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-207_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 35% complete for Sample_3266-CB-107.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-86_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
q.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-180.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-64_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-64_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
/nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-64_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-64_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 35% complete for Sample_3266-CB-107.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-180.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-96_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-75_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 90% complete for Sample_3266-CB-180.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-77_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 55% complete for Sample_3266-CB-107.R1.fq.gz
pprox 95% complete for Sample_3266-CB-180.R2.fq.gz
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
fq.gz
Approx 40% complete for Sample_3266-CB-107.R2.fq.gz
33.78%) Forward Only Surviving: 16806521 (65.74%) Reverse Only Surviving: 40857 (0.16%) Dropped: 83354 (0.33%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 04:39:21 2023]
Finished job 0.
1 of 1 steps (100%) done
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-57_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Waiting at most 60 seconds for missing files.
Approx 60% complete for Sample_3266-CB-107.R1.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-98_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-180_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 65% complete for Sample_3266-CB-107.R2.fq.gz
Approx 65% complete for Sample_3266-CB-107.R1.fq.gz
Approx 70% complete for Sample_3266-CB-107.R2.fq.gz
Approx 70% complete for Sample_3266-CB-107.R1.fq.gz
Approx 60% complete for Sample_3266-CB-107.R1.fq.gz
33.78%) Forward Only Surviving: 16806521 (65.74%) Reverse Only Surviving: 40857 (0.16%) Dropped: 83354 (0.33%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 04:44:21 2023]
Finished job 0.
1 of 1 steps (100%) done
Approx 75% complete for Sample_3266-CB-107.R1.fq.gz
Approx 80% complete for Sample_3266-CB-107.R1.fq.gz
Approx 85% complete for Sample_3266-CB-107.R1.fq.gz
Approx 90% complete for Sample_3266-CB-107.R1.fq.gz
Approx 75% complete for Sample_3266-CB-107.R2.fq.gz
Approx 95% complete for Sample_3266-CB-107.R1.fq.gz
Approx 80% complete for Sample_3266-CB-107.R2.fq.gz
Waiting at most 60 seconds for missing files.
Approx 90% complete for Sample_3266-CB-107.R1.fq.gz
(29.57%) Forward Only Surviving: 26627441 (69.76%) Reverse Only Surviving: 89995 (0.24%) Dropped: 167448 (0.44%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 04:53:09 2023]
Finished job 0.
1 of 1 steps (100%) done
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Approx 85% complete for Sample_3266-CB-107.R2.fq.gz
Approx 95% complete for Sample_3266-CB-107.R1.fq.gz
Approx 90% complete for Sample_3266-CB-107.R2.fq.gz
Waiting at most 60 seconds for missing files.
Approx 95% complete for Sample_3266-CB-107.R2.fq.gz
urbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R1_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R1_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Input Read Pairs: 38171493 Both Surviving: 11286609 (29.57%) Forward Only Surviving: 26627441 (69.76%) Reverse Only Surviving: 89995 (0.24%) Dropped: 167448 (0.44%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 04:58:10 2023]
Finished job 0.
1 of 1 steps (100%) done
Waiting at most 60 seconds for missing files.
MissingOutputException in rule fastqc in file /nfs/turbo/remillsscr/wenjingu/standard_pipelines/call_SNP_RNA-seq/RNA-Seq-Variant-Calling/Snakefile, line 49:
Job 0 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R2_fastqc.html
/home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA/qc_output/Sample_3266-CB-107_R2_fastqc.zip
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Input Read Pairs: 55558520 Both Surviving: 18514939 (33.33%) Forward Only Surviving: 36694681 (66.05%) Reverse Only Surviving: 124440 (0.22%) Dropped: 224460 (0.40%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 04:59:48 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 52954269 Both Surviving: 19551950 (36.92%) Forward Only Surviving: 33086032 (62.48%) Reverse Only Surviving: 123897 (0.23%) Dropped: 192390 (0.36%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:00:13 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 56920823 Both Surviving: 24291530 (42.68%) Forward Only Surviving: 32312532 (56.77%) Reverse Only Surviving: 138323 (0.24%) Dropped: 178438 (0.31%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:03:39 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 62083123 Both Surviving: 21767785 (35.06%) Forward Only Surviving: 40073216 (64.55%) Reverse Only Surviving: 94707 (0.15%) Dropped: 147415 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:04:46 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 58580235 Both Surviving: 27549445 (47.03%) Forward Only Surviving: 30713474 (52.43%) Reverse Only Surviving: 146353 (0.25%) Dropped: 170963 (0.29%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:04:47 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 58452416 Both Surviving: 18271295 (31.26%) Forward Only Surviving: 39827412 (68.14%) Reverse Only Surviving: 123182 (0.21%) Dropped: 230527 (0.39%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:05:16 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 70105728 Both Surviving: 42420405 (60.51%) Forward Only Surviving: 27057668 (38.60%) Reverse Only Surviving: 309506 (0.44%) Dropped: 318149 (0.45%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:05:38 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 52954269 Both Surviving: 19551950 (36.92%) Forward Only Surviving: 33086032 (62.48%) Reverse Only Surviving: 123897 (0.23%) Dropped: 192390 (0.36%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:05:41 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 52821384 Both Surviving: 18039220 (34.15%) Forward Only Surviving: 34434450 (65.19%) Reverse Only Surviving: 122577 (0.23%) Dropped: 225137 (0.43%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:06:09 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 55558520 Both Surviving: 18514939 (33.33%) Forward Only Surviving: 36694681 (66.05%) Reverse Only Surviving: 124440 (0.22%) Dropped: 224460 (0.40%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:08:59 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 58452416 Both Surviving: 18271295 (31.26%) Forward Only Surviving: 39827412 (68.14%) Reverse Only Surviving: 123182 (0.21%) Dropped: 230527 (0.39%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:10:28 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 60317187 Both Surviving: 21689781 (35.96%) Forward Only Surviving: 38363865 (63.60%) Reverse Only Surviving: 105340 (0.17%) Dropped: 158201 (0.26%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:10:48 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 70105728 Both Surviving: 42420405 (60.51%) Forward Only Surviving: 27057668 (38.60%) Reverse Only Surviving: 309506 (0.44%) Dropped: 318149 (0.45%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:10:49 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 75701110 Both Surviving: 44391439 (58.64%) Forward Only Surviving: 30848909 (40.75%) Reverse Only Surviving: 236231 (0.31%) Dropped: 224531 (0.30%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:11:03 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 52821384 Both Surviving: 18039220 (34.15%) Forward Only Surviving: 34434450 (65.19%) Reverse Only Surviving: 122577 (0.23%) Dropped: 225137 (0.43%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:11:31 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 56920823 Both Surviving: 24291530 (42.68%) Forward Only Surviving: 32312532 (56.77%) Reverse Only Surviving: 138323 (0.24%) Dropped: 178438 (0.31%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:12:53 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 81142448 Both Surviving: 51657386 (63.66%) Forward Only Surviving: 28773897 (35.46%) Reverse Only Surviving: 357413 (0.44%) Dropped: 353752 (0.44%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:13:05 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 62083123 Both Surviving: 21767785 (35.06%) Forward Only Surviving: 40073216 (64.55%) Reverse Only Surviving: 94707 (0.15%) Dropped: 147415 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:14:32 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 58580235 Both Surviving: 27549445 (47.03%) Forward Only Surviving: 30713474 (52.43%) Reverse Only Surviving: 146353 (0.25%) Dropped: 170963 (0.29%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:14:59 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 60317187 Both Surviving: 21689781 (35.96%) Forward Only Surviving: 38363865 (63.60%) Reverse Only Surviving: 105340 (0.17%) Dropped: 158201 (0.26%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:15:58 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 65256356 Both Surviving: 31217503 (47.84%) Forward Only Surviving: 33782597 (51.77%) Reverse Only Surviving: 118757 (0.18%) Dropped: 137499 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:17:24 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 67242040 Both Surviving: 46421924 (69.04%) Forward Only Surviving: 20464944 (30.43%) Reverse Only Surviving: 213966 (0.32%) Dropped: 141206 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:17:31 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 81142448 Both Surviving: 51657386 (63.66%) Forward Only Surviving: 28773897 (35.46%) Reverse Only Surviving: 357413 (0.44%) Dropped: 353752 (0.44%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:18:09 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 63879300 Both Surviving: 26061664 (40.80%) Forward Only Surviving: 37553789 (58.79%) Reverse Only Surviving: 113490 (0.18%) Dropped: 150357 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:19:22 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 78638811 Both Surviving: 54136817 (68.84%) Forward Only Surviving: 23847974 (30.33%) Reverse Only Surviving: 344767 (0.44%) Dropped: 309253 (0.39%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:20:00 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 75701110 Both Surviving: 44391439 (58.64%) Forward Only Surviving: 30848909 (40.75%) Reverse Only Surviving: 236231 (0.31%) Dropped: 224531 (0.30%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:20:24 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 76819574 Both Surviving: 34626492 (45.08%) Forward Only Surviving: 41907158 (54.55%) Reverse Only Surviving: 125078 (0.16%) Dropped: 160846 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:20:46 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 67242040 Both Surviving: 46421924 (69.04%) Forward Only Surviving: 20464944 (30.43%) Reverse Only Surviving: 213966 (0.32%) Dropped: 141206 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:22:19 2023]
Finished job 0.
1 of 1 steps (100%) done
Only Surviving: 33782597 (51.77%) Reverse Only Surviving: 118757 (0.18%) Dropped: 137499 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:22:19 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 63879300 Both Surviving: 26061664 (40.80%) Forward Only Surviving: 37553789 (58.79%) Reverse Only Surviving: 113490 (0.18%) Dropped: 150357 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:24:25 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 76819574 Both Surviving: 34626492 (45.08%) Forward Only Surviving: 41907158 (54.55%) Reverse Only Surviving: 125078 (0.16%) Dropped: 160846 (0.21%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:27:04 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 78638811 Both Surviving: 54136817 (68.84%) Forward Only Surviving: 23847974 (30.33%) Reverse Only Surviving: 344767 (0.44%) Dropped: 309253 (0.39%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:31:00 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 89732041 Both Surviving: 58374707 (65.05%) Forward Only Surviving: 31000457 (34.55%) Reverse Only Surviving: 195610 (0.22%) Dropped: 161267 (0.18%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:32:09 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 86059117 Both Surviving: 49892103 (57.97%) Forward Only Surviving: 35776191 (41.57%) Reverse Only Surviving: 182928 (0.21%) Dropped: 207895 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:32:44 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 83724507 Both Surviving: 49078315 (58.62%) Forward Only Surviving: 33948935 (40.55%) Reverse Only Surviving: 346549 (0.41%) Dropped: 350708 (0.42%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:36:06 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 86059117 Both Surviving: 49892103 (57.97%) Forward Only Surviving: 35776191 (41.57%) Reverse Only Surviving: 182928 (0.21%) Dropped: 207895 (0.24%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:37:33 2023]
Finished job 0.
1 of 1 steps (100%) done
Input Read Pairs: 83724507 Both Surviving: 49078315 (58.62%) Forward Only Surviving: 33948935 (40.55%) Reverse Only Surviving: 346549 (0.41%) Dropped: 350708 (0.42%)
TrimmomaticPE: Completed successfully
[Mon Nov 6 05:41:04 2023]
Finished job 0.
1 of 1 steps (100%) done