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CCBR / XAVIER

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
https://ccbr.github.io/XAVIER/
MIT License
1 stars 3 forks source link

numerous jobs failing with v3.0.2 #79

Closed kelly-sovacool closed 10 months ago

kelly-sovacool commented 10 months ago

xavier command:

module load ccbrpipeliner
xavier run \
  --input /data/CCBR_Pipeliner/Pipelines/XAVIER/v3.0/.tests/*.fastq.gz \
  --output /data/sovacoolkl/xavier_test_v3.0.2 \
  --genome hg38 \
  --targets /data/CCBR_Pipeliner/Pipelines/XAVIER/v3.0/.tests/Agilent_SSv7_allExons_hg38.bed \
  --mode slurm \
  --runmode run

logfiles/snakemake.log.jobby.short:

jobname state   std_err
trimmomatic.samples=Sample11_ACI_158_S38    COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347872.trimmomatic.samples=Sample11_ACI_158_S38.err
fc_lane.samples=Sample10_ARK1_S37   COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347874.fc_lane.samples=Sample10_ARK1_S37.err
trimmomatic.samples=Sample10_ARK1_S37   COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347878.trimmomatic.samples=Sample10_ARK1_S37.err
fc_lane.samples=Sample11_ACI_158_S38    COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347880.fc_lane.samples=Sample11_ACI_158_S38.err
trimmomatic.samples=Sample4_CRL1622_S31 COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347882.trimmomatic.samples=Sample4_CRL1622_S31.err
fc_lane.samples=Sample4_CRL1622_S31 COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18347885.fc_lane.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348010.fastq_screen.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348013.kraken.samples=Sample11_ACI_158_S38.err
bwa_mem.samples=Sample11_ACI_158_S38    COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348016.bwa_mem.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348018.kraken.samples=Sample10_ARK1_S37.err
bwa_mem.samples=Sample10_ARK1_S37   COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348020.bwa_mem.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348023.fastq_screen.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348026.kraken.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348028.fastq_screen.samples=Sample10_ARK1_S37.err
bwa_mem.samples=Sample4_CRL1622_S31 COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348031.bwa_mem.samples=Sample4_CRL1622_S31.err
gatk_recal.samples=Sample10_ARK1_S37    COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348202.gatk_recal.samples=Sample10_ARK1_S37.err
gatk_recal.samples=Sample4_CRL1622_S31  COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348205.gatk_recal.samples=Sample4_CRL1622_S31.err
gatk_recal.samples=Sample11_ACI_158_S38 COMPLETED   /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348210.gatk_recal.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348285.kraken.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348288.kraken.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348446.kraken.samples=Sample10_ARK1_S37.err
bam_check.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348500.bam_check.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348503.bam2fastq.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348506.bam2fastq.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348510.bam_check.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348513.bam2fastq.samples=Sample4_CRL1622_S31.err
bam_check.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348517.bam_check.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348550.fastq_screen.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348554.fastq_screen.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348558.fastq_screen.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348732.kraken.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348757.kraken.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348778.kraken.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348781.fastq_screen.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348785.fastq_screen.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348788.bam2fastq.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348791.bam_check.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348795.bam2fastq.samples=Sample10_ARK1_S37.err
bam_check.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348798.bam_check.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348802.bam_check.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348805.fastq_screen.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348808.bam2fastq.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348981.bam2fastq.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348984.fastq_screen.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348986.bam2fastq.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348989.bam2fastq.samples=Sample10_ARK1_S37.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348992.kraken.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348994.kraken.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348996.fastq_screen.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348997.fastq_screen.samples=Sample4_CRL1622_S31.err
bam_check.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348999.bam_check.samples=Sample10_ARK1_S37.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349001.kraken.samples=Sample4_CRL1622_S31.err
bam_check.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349003.bam_check.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349006.bam_check.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349138.bam2fastq.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349141.bam_check.samples=Sample10_ARK1_S37.err
bam2fastq.samples=Sample10_ARK1_S37 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349143.bam2fastq.samples=Sample10_ARK1_S37.err
bam_check.samples=Sample11_ACI_158_S38  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349144.bam_check.samples=Sample11_ACI_158_S38.err
bam_check.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349146.bam_check.samples=Sample4_CRL1622_S31.err
bam2fastq.samples=Sample4_CRL1622_S31   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18349147.bam2fastq.samples=Sample4_CRL1622_S31.err
kelly-sovacool commented 10 months ago

Error from kraken

(/gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/logfiles/slurmfiles/18346496.18348013.kraken.samples=Sample11_ACI_158_S38.err)

Loading database information... done.
0 sequences (0.00 Mbp) processed in 0.000s (0.0 Kseq/m, 0.00 Mbp/m).
  0 sequences classified (-nan%)
  0 sequences unclassified (-nan%)
cut: /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2/QC/kraken/Sample11_ACI_158_S38.trimmed.kraken_bacteria.out.txt: No such file or directory
kelly-sovacool commented 10 months ago

Another test run with --pairs still resulted in errors:

xavier run \
  --input /data/CCBR_Pipeliner/Pipelines/XAVIER/v3.0/.tests/*.fastq.gz \
  --output /data/sovacoolkl/xavier_test_v3.0.2_2 \
  --pairs /data/CCBR_Pipeliner/Pipelines/XAVIER/v3.0/.tests/pairs.tsv \
  --genome hg38 \
  --targets /data/CCBR_Pipeliner/Pipelines/XAVIER/v3.0/.tests/Agilent_SSv7_allExons_hg38.bed \
  --mode slurm \
  --runmode run

cat xavier_test_v3.0.2_2/logfiles/snakemake.log.jobby.short | grep FAILED:

fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364285.fastq_screen.samples=Sample10_ARK1_S37.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364287.kraken.samples=Sample10_ARK1_S37.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364289.kraken.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364293.fastq_screen.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364297.kraken.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364299.fastq_screen.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364369.kraken.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364371.kraken.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364379.kraken.samples=Sample10_ARK1_S37.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364468.kraken.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364470.kraken.samples=Sample10_ARK1_S37.err
qualimap_bamqc.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364498.qualimap_bamqc.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364545.fastq_screen.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364552.fastq_screen.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364565.fastq_screen.samples=Sample4_CRL1622_S31.err
qualimap_bamqc.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364618.qualimap_bamqc.samples=Sample10_ARK1_S37.err
qualimap_bamqc.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364620.qualimap_bamqc.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364976.kraken.samples=Sample10_ARK1_S37.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18364994.kraken.samples=Sample11_ACI_158_S38.err
kraken.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365012.kraken.samples=Sample4_CRL1622_S31.err
qualimap_bamqc.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365121.qualimap_bamqc.samples=Sample4_CRL1622_S31.err
qualimap_bamqc.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365303.qualimap_bamqc.samples=Sample11_ACI_158_S38.err
qualimap_bamqc.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365523.qualimap_bamqc.samples=Sample4_CRL1622_S31.err
kraken.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365527.kraken.samples=Sample11_ACI_158_S38.err
qualimap_bamqc.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365547.qualimap_bamqc.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365549.fastq_screen.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365551.fastq_screen.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365557.fastq_screen.samples=Sample11_ACI_158_S38.err
qualimap_bamqc.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365576.qualimap_bamqc.samples=Sample11_ACI_158_S38.err
qualimap_bamqc.samples=Sample11_ACI_158_S38 FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365687.qualimap_bamqc.samples=Sample11_ACI_158_S38.err
qualimap_bamqc.samples=Sample4_CRL1622_S31  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365691.qualimap_bamqc.samples=Sample4_CRL1622_S31.err
qualimap_bamqc.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365703.qualimap_bamqc.samples=Sample10_ARK1_S37.err
qualimap_bamqc.samples=Sample10_ARK1_S37    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18365967.qualimap_bamqc.samples=Sample10_ARK1_S37.err
fastq_screen.samples=Sample11_ACI_158_S38   FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18366199.fastq_screen.samples=Sample11_ACI_158_S38.err
fastq_screen.samples=Sample4_CRL1622_S31    FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18366201.fastq_screen.samples=Sample4_CRL1622_S31.err
fastq_screen.samples=Sample10_ARK1_S37  FAILED  /gpfs/gsfs12/users/sovacoolkl/xavier_test_v3.0.2_2/logfiles/slurmfiles/18362940.18366203.fastq_screen.samples=Sample10_ARK1_S37.err
kelly-sovacool commented 10 months ago

The actual problem is the fastq files in .tests/ are blank 🤦🏻‍♀️

kelly-sovacool commented 10 months ago

it is actually running successfully with real data