mkfifo: cannot create fifo : Operation not supported

[rashidma]

I have installed nextneopi using WSL. With your help, I managed to troubleshoot many errors but so far I could not run successfully the example data. Please see new error about named pipes:

Error executing process > 'mhc_extract (test)'

Caused by:
  Process `mhc_extract (test)` terminated with an error exit status (1)

Command executed:

  rm -f unmapped_bam mhc_mapped_bam R1.fastq R2.fastq
  mkfifo unmapped_bam
  mkfifo mhc_mapped_bam
  mkfifo R1.fastq
  mkfifo R2.fastq

  samtools  view -@4 -h -b -u -f 4 test_tumor_DNA_aligned_sort_mkdp.bam > unmapped_bam &
  samtools  view -@4 -h -b -u test_tumor_DNA_aligned_sort_mkdp.bam chr6:28510120-33480577 > mhc_mapped_bam &

  samtools merge -@4 -u - mhc_mapped_bam unmapped_bam | \
      samtools sort -@4 -n - | \
      samtools fastq -@2 -1 R1.fastq -2 R2.fastq -s /dev/null -0 /dev/null - &
  perl -ple 'if (($. % 4) == 1) { s/$/ 1:N:0:NNNNNNNN/; }' R1.fastq | gzip -1 > test_reads_mhc_R1.fastq.gz &
  perl -ple 'if (($. % 4) == 1) { s/$/ 2:N:0:NNNNNNNN/; }' R2.fastq | gzip -1 > test_reads_mhc_R2.fastq.gz &

  wait

  rm -f unmapped_bam mhc_mapped_bam R1.fastq R2.fastq

Command exit status:
  1

Command output:
  (empty)

Command error:
  mkfifo: cannot create fifo 'unmapped_bam': Operation not supported

Work dir:
  /mnt/e/Mamoon/NRC21R-082-03/Analysis/nextNEOpi/demo/work/2a/c32b1869284e840298e29f00539fa7

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

Please let me know how to solve this issue.

Many thanks

[riederd]

Hi,

I have no experience with WSL so I can just guess. From a Google search it seems that you need to enable metadata in order to get support for fifos.

See: https://devblogs.microsoft.com/commandline/chmod-chown-wsl-improvements/

HTH

[riederd]

No feedback, assuming the issue as solved