samplesheet error

[Laura Uelze]

Description of the bug

I am getting a sample sheet error with the following sample sheet:

sample,fastq_1,fastq_2
HIC_ES_4,/lustre/projects/dazzlerAssembly/test_hic/SRR5339783_1.fastq.gz,/lustre/projects/dazzlerAssembly/test_hic/SRR5339783_2.fastq.gz

The error may be related to #152, but as there is only one line in my sample sheet it seems unlikely.

Another potential problem could be that our system does not have file locks. However, I thought I took care of that by using the -w /tmp/ flag. (/tmp/ does have file locks!).
Any other idea what I could try?

Perhaps singularity is missing some bind? (because of the message /tmp/1c/167b78c8be41694d24c476732df8e2 doesn't exist in container) Is it possible to specify a singularity bind?
I cant use docker, as we cannot install docker on our system.

Command used and terminal output

nextflow run nf-core/hic --input /lustre/projects/dazzlerAssembly/test_hic/samplesheet.csv --outdir /lustre/projects/dazzlerAssembly/test_hic/hic_results --genome GRCh37 -profile singularity -w /tmp/ --digestion hindiii


-[nf-core/hic] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /tmp/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)'

Caused by:
  Process `NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (255)

Command executed:

  check_samplesheet.py \
      samplesheet.csv \
      samplesheet.valid.csv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /tmp/1c/167b78c8be41694d24c476732df8e2 [cwd]: /tmp/1c/167b78c8be41694d24c476732df8e2 doesn't exist in container
  WARNING: Skipping mount /lustre/sw/apps/singularity/3.5.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  FATAL:   container creation failed: mount /tmp/1c/167b78c8be41694d24c476732df8e2->/tmp/1c/167b78c8be41694d24c476732df8e2 error: while mounting /tmp/1c/167b78c8be41694d24c476732df8e2: destination /tmp/1c/167b78c8be41694d24c476732df8e2 doesn't exist in container

Work dir:
  /tmp/1c/167b78c8be41694d24c476732df8e2

Relevant files

No response

System information

nextflow version 23.04.4.5881
openjdk 17.0.8-internal 2023-07-18
HPC
Singularity
Linux
nextflow pull nf-core/hic
Checking nf-core/hic ...
Already-up-to-date - revision: fe4ac65 [master]

[kexingai]

Hi Alca,

I encountered the same issue. Did you find the solution for it?
Thanks,

[Nicolas Servant]

Hi,
I think this is a general singularity issue, not really a samplesheet one.
Did you already use any other nf-core pipeline with singularity ?

[Nicolas Servant]

linked to #180