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error_snakemake2
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error_snakemake2
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rule Trim:
input: B_EmbrioTransfer_84_S12_R1_001.fastq.gz, B_EmbrioTransfer_84_S12_R3_001.fastq.gz
output: Trim_Galore/B_EmbrioTransfer_84_S12_R1_001_val_1.fq.gz, Trim_Galore/B_EmbrioTransfer_84_S12_R3_001_val_2.fq.gz, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt
jobid: 76
wildcards: b=B_EmbrioTransfer_84_S12
threads: 10
resources: mem_mb=32000
/TrimGalore*/trim_galore --paired --output_dir ./Trim_Galore -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC B_EmbrioTransfer_84_S12_R1_001.fastq.gz B_EmbrioTransfer_84_S12_R3_001.fastq.gz &>> Reports/Trim_Galore/Trim_Log.txt && mv Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt Reports/Trim_Galore/
[Sat Sep 8 11:34:26 2018]
Error in rule Trim:
jobid: 76
output: Trim_Galore/B_EmbrioTransfer_84_S12_R1_001_val_1.fq.gz, Trim_Galore/B_EmbrioTransfer_84_S12_R3_001_val_2.fq.gz, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt
RuleException:
CalledProcessError in line 57 of /Analysis/Snakefile:
Command ' set -euo pipefail; /TrimGalore*/trim_galore --paired --output_dir ./Trim_Galore -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC B_EmbrioTransfer_84_S12_R1_001.fastq.gz B_EmbrioTransfer_84_S12_R3_001.fastq.gz &>> Reports/Trim_Galore/Trim_Log.txt && mv Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt Reports/Trim_Galore/ ' returned non-zero exit status 1.
File "/Analysis/Snakefile", line 57, in __rule_Trim
File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
[Sat Sep 8 11:39:49 2018]
Finished job 127.
1 of 161 steps (0.62%) done
[Sat Sep 8 12:53:28 2018]
Finished job 42.
2 of 161 steps (1%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /Analysis/.snakemake/log/2018-09-08T111516.223202.snakemake.log
###################################################################################################
[Sat Sep 8 09:00:56 2018]
rule Trim:
input: B_EmbrioTransfer_84_S12_R1_001.fastq.gz, B_EmbrioTransfer_84_S12_R3_001.fastq.gz
output: Trim_Galore/B_EmbrioTransfer_84_S12_R1_001_val_1.fq.gz, Trim_Galore/B_EmbrioTransfer_84_S12_R3_001_val_2.fq.gz, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt
jobid: 62
wildcards: b=B_EmbrioTransfer_84_S12
threads: 10
resources: mem_mb=32000
/TrimGalore*/trim_galore --paired --output_dir ./Trim_Galore -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC B_EmbrioTransfer_84_S12_R1_001.fastq.gz B_EmbrioTransfer_84_S12_R3_001.fastq.gz &>> Reports/Trim_Galore/Trim_Log.txt && mv Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt Reports/Trim_Galore/
[Sat Sep 8 09:00:56 2018]
rule Diversity:
input: Trim_Galore/B_Control-NM_42_S13_R1_001_val_1.fq.gz, Trim_Galore/B_Control-NM_42_S13_R3_001_val_2.fq.gz
output: Diversity/B_Control-NM_42_S13_R1_001_val_1.fq_trimmed.fq.gz, Diversity/B_Control-NM_42_S13_R3_001_val_2.fq_trimmed.fq.gz
jobid: 43
wildcards: b=B_Control-NM_42_S13
threads: 10
resources: mem_mb=32000
python /trimRRBSdiversityAdaptCustomers.py -1 Trim_Galore/B_Control-NM_42_S13_R1_001_val_1.fq.gz -2 Trim_Galore/B_Control-NM_42_S13_R3_001_val_2.fq.gz &>> Reports/Diversity_Log.txt && mv Trim_Galore/B_Control-NM_42_S13_R1_001_val_1.fq_trimmed.fq.gz Trim_Galore/B_Control-NM_42_S13_R3_001_val_2.fq_trimmed.fq.gz ./Diversity/
[Sat Sep 8 09:00:56 2018]
rule Trim:
input: B_IVculture_27_S2_R1_001.fastq.gz, B_IVculture_27_S2_R3_001.fastq.gz
output: Trim_Galore/B_IVculture_27_S2_R1_001_val_1.fq.gz, Trim_Galore/B_IVculture_27_S2_R3_001_val_2.fq.gz, Reports/Trim_Galore/B_IVculture_27_S2_R1_001.fastq.gz_trimming_report.txt, Reports/Trim_Galore/B_IVculture_27_S2_R3_001.fastq.gz_trimming_report.txt
jobid: 109
wildcards: b=B_IVculture_27_S2
threads: 10
resources: mem_mb=32000
/TrimGalore*/trim_galore --paired --output_dir ./Trim_Galore -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC B_IVculture_27_S2_R1_001.fastq.gz B_IVculture_27_S2_R3_001.fastq.gz &>> Reports/Trim_Galore/Trim_Log.txt && mv Trim_Galore/B_IVculture_27_S2_R1_001.fastq.gz_trimming_report.txt Trim_Galore/B_IVculture_27_S2_R3_001.fastq.gz_trimming_report.txt Reports/Trim_Galore/
[Sat Sep 8 09:20:27 2018]
Error in rule Trim:
jobid: 62
output: Trim_Galore/B_EmbrioTransfer_84_S12_R1_001_val_1.fq.gz, Trim_Galore/B_EmbrioTransfer_84_S12_R3_001_val_2.fq.gz, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt, Reports/Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt
RuleException:
CalledProcessError in line 57 of /Analysis/Snakefile:
Command ' set -euo pipefail; /TrimGalore*/trim_galore --paired --output_dir ./Trim_Galore -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC B_EmbrioTransfer_84_S12_R1_001.fastq.gz B_EmbrioTransfer_84_S12_R3_001.fastq.gz &>> Reports/Trim_Galore/Trim_Log.txt && mv Trim_Galore/B_EmbrioTransfer_84_S12_R1_001.fastq.gz_trimming_report.txt Trim_Galore/B_EmbrioTransfer_84_S12_R3_001.fastq.gz_trimming_report.txt Reports/Trim_Galore/ ' returned non-zero exit status 1.
File "/Analysis/Snakefile", line 57, in __rule_Trim
File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
[Sat Sep 8 09:26:18 2018]
Finished job 109.
1 of 163 steps (0.61%) done
[Sat Sep 8 10:41:16 2018]
Finished job 43.
2 of 163 steps (1%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message