sarek cnv erro

cnv erro

Open ld9866 opened this issue 2 years ago • 1 comments

Description of the bug

Hello dear software developers: I used sarek to process our sequencing data, and it showed very good performance in the process of generating bam files, and then recently we encountered some problems when running cnv files. As I uploaded the file, I am running snp, inde and sv without any problem, but at present it reported such an error, I hope you can help me find out what is the problem? Best day!

Command used and terminal output

nextflow run /home/lidong/nextflow/sarek-3.0-pig/ --genome susScr3 --input CNV.csv --step variant_calling  --tools cnvkit --outdir ./ -profile docker

-[nf-core/sarek] Pipeline completed with errors-
Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (GCF_000003025.6_Sscrofa11.1_genomic.fna)'

Caused by:
  Process `NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (GCF_000003025.6_Sscrofa11.1_genomic.fna)` terminated with an error exit status (127)

Command executed:

  samtools \
      faidx \
      GCF_000003025.6_Sscrofa11.1_genomic.fna
 
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  docker: Error response from daemon: failed to create shim: OCI runtime create failed: container_linux.go:380: starting container process caused: process_linux.go:545: container init caused: rootfs_linux.go:75: mounting "/etc/passwd" to rootfs at "/etc/passwd" caused: mount through procfd: no such file or directory: unknown.
  time="2022-07-29T10:37:43+08:00" level=error msg="error waiting for container: context canceled"

Work dir:
  /home/lidong/nextflow/PRJEB1683/csv/work/e4/645ccc15404fbdcbaa5fb92a08dbf2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line