Error executing process > 'VC:varscan_tonly (9)'

[samarth8392]

Description of the bug

Error executing process > 'VC:varscan_tonly (9)'

Caused by:
  Process `VC:varscan_tonly (9)` terminated with an error exit status (255)


Command executed:

  varscan_opts="--strand-filter 0 --min-var-freq 0.01 --output-vcf 1 --variants 1"
      pileup_cmd="samtools mpileup -d 100000 -q 15 -Q 15 -f /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/bwamem2/GRCh38.d1.vd1.fa -l 106.bed WGS_NC_T.bqsr.bam"
      varscan_cmd="varscan mpileup2cns <($pileup_cmd) $varscan_opts"
  
      eval "$varscan_cmd > WGS_NC_T_106.tonly.varscan.vcf_temp"
  
      awk '{{gsub(/\y[W|K|Y|R|S|M|B|D|H|V]\y/,"N",$4); OFS = "	"; print}}' WGS_NC_T_106.tonly.varscan.vcf_temp         | sed '/^$/d' | bcftools view - -Oz -o WGS_NC_T_106.tonly.varscan.vcf
  
      printf "Sample1	WGS_NC_T
  " > sampname
  
      bcftools reheader -s sampname WGS_NC_T_106.tonly.varscan.vcf         | bcftools view -Oz -o WGS_NC_T_106.tonly.varscan.vcf.gz

Command exit status:
  255

Command output:
  (empty)

Command error:
WARNING: While bind mounting '/gs10:/gs10': destination is already in the mount point list
  WARNING: While bind mounting '/gs11:/gs11': destination is already in the mount point list
  WARNING: While bind mounting '/gs12:/gs12': destination is already in the mount point list
  WARNING: While bind mounting '/spin1:/spin1': destination is already in the mount point list
  WARNING: While bind mounting '/fdb:/fdb': destination is already in the mount point list
  WARNING: While bind mounting '/gpfs:/gpfs': destination is already in the mount point list
  [mpileup] 1 samples in 1 input files
  Only variants will be reported
  Warning: No p-value threshold provided, so p-values will not be calculated
  Min coverage:	8
  Min reads2:	2
  Min var freq:	0.01
  Min avg qual:	15
  P-value thresh:	0.01
  Reading input from /dev/fd/63
  0 bases in pileup file
  0 variant positions (0 SNP, 0 indel)
  0 were failed by the strand-filter
  0 variant positions reported (0 SNP, 0 indel)
  Failed to read from standard input: unknown file type

Work dir:
  /vf/users/CCBR/projects/techDev/runs/work/97/f56f2b9d9680bb32464d86cd48cfd4

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Command used and terminal output

nextflow run /data/CCBR/projects/techDev/LOGAN/main.nf \
--mode slurm -profile biowulf,slurm \
--genome hg38 \
--sample_sheet /data/CCBR/projects/techDev/logan_pairs.txt \
--outdir /data/CCBR/projects/techDev/runs/logan_test \
--fastq_file_input /data/CCBR/projects/techDev/logan_fastq_input.txt \
--vc --sv --cnv -resume 56384b13439f38b11c3f2dfbe3e18ce5

Relevant files

execution_report_2025-01-28_21-28-01.html.zip

System information

No response