Error at cram_cache

[stfacc]

Operating System

Other Linux (please specify below)

Other Linux

Ubuntu 20.04

Workflow Version

v1.9.0-g78f5a87

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

BAM="/home/sfacchini/mnt/rd013s/230813_Andrea_WGS_analysis/bam/61552/61552.bam"
REF="/data/kronos/kronos/sfacchini/reference/Homo_sapiens_assembly38.fasta"

nextflow run epi2me-labs/wf-human-variation \
      --bam $BAM \
      --ref $REF \
      --sample_name "sample_61552" \
      --snp \
      --sv \
      --cnv \
      --str \
      --phase_vcf \
      --sv_benchmark \
      --threads 64

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Immediately stop at cram_cache phase.

If I cd to the workdir and run bash .command.run I get the same error, but running the command seq_cache_populate.pl -root ref_cache/ Homo_sapiens_assembly38.fasta directly works.

Note that /data/kronos, where the reference is located, is actually a different mountpoint

Relevant log output

ERROR ~ Error executing process > 'cram_cache (1)'

Caused by:
  Process `cram_cache (1)` terminated with an error exit status (13)

Command executed:

  # Invoke from binary installed to container PATH
  seq_cache_populate.pl -root ref_cache/ Homo_sapiens_assembly38.fasta
  REF_PATH="ref_cache/%2s/%2s/%s"

Command exit status:
  13

Command output:
  (empty)

Command error:
  Couldn't open Homo_sapiens_assembly38.fasta: Permission denied

Work dir:
  /data/array/sfacchini/wf-human-variation_test/work/f9/20496a31437f8bb88cbbc9599f8002

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

 -- Check '.nextflow.log' file for details

Application activity log entry

No response

[RenzoTale88]

Hi @stfacc do you have rw permissions for the file?

ls -al /data/kronos/kronos/sfacchini/reference/Homo_sapiens_assembly38.fasta

You can try and check whether you get the same error if you copy the fasta file locally and pass that as --ref:

cp /data/kronos/kronos/sfacchini/reference/Homo_sapiens_assembly38.fasta /home/sfacchini/mnt/rd013s/230813_Andrea_WGS_analysis/

And then:

BAM="/home/sfacchini/mnt/rd013s/230813_Andrea_WGS_analysis/bam/61552/61552.bam"
REF="/home/sfacchini/mnt/rd013s/230813_Andrea_WGS_analysis/Homo_sapiens_assembly38.fasta"

nextflow run epi2me-labs/wf-human-variation \
      --bam $BAM \
      --ref $REF \
      --sample_name "sample_61552" \
      --snp \
      --sv \
      --cnv \
      --str \
      --phase_vcf \
      --sv_benchmark \
      --threads 64

[stfacc]

Yes, copying the ref. locally works, but I can usually access the file without issues. Moreover, doing:

$ cd work/f9/20496a31437f8bb88cbbc9599f8002
$ seq_cache_populate.pl -root ref_cache/ Homo_sapiens_assembly38.fasta

works, too. So it's something with docker configuration?

Is there a discord or slack channel in case I have more questions, instead of creating reports here?

Thank you!

[RenzoTale88]

@stfacc yes, it has to do with the docker configuration in your system. By default, the profile adds the --user \$(id -u):\$(id -g) --group-add 100, but your system might require more configuration to properly access the desired path, for which you'd need help from your system admin to properly make it run. We can help you with defining a custom configuration if needed.

I'm afraid we do not have neither a slack or discord channel to contact us directly. We regularly monitor our GitHub repositories though, so please open more tickets to get support from us if needed.

[SamStudio8]

Closing due to lack of response, please get in touch if you're still running in to trouble!