FAQCs repeatedly failing with Exit Code 1 - causing pipeline to fail

[snallani-msdh]

Hello,

We have just started trying to implement this pipeline on some samples from MS which were sequenced by the CDC. I downloaded the fastq files from NCBI and have started trying to process them.

I have the latest versions of Nextflow and Java installed. I used the automated samplesheet creation instructions from the usage guide to create the sample sheet. When I run the pipeline, however, the FAQCs preprocess exits repeatedly with exit code 1. I thought that maybe it was because it needed more resources and created a custom config file to set mem to 50GB, but the error is still occuring.

The error message reads:

`-[CDCgov/mycosnp-nf] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:FAQCS (SRR26957882)'

Caused by: Process NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:FAQCS (SRR26957882) terminated with an error exit status (1)

Command executed:

[ ! -f SRR26957882_1.fastq.gz ] && ln -s SRR26957882_R1.paired.fastq.gz SRR26957882_1.fastq.gz [ ! -f SRR26957882_2.fastq.gz ] && ln -s SRR26957882_R2.paired.fastq.gz SRR26957882_2.fastq.gz FaQCs \ -d . \ -1 SRR26957882_1.fastq.gz \ -2 SRR26957882_2.fastq.gz \ --prefix SRR26957882 \ -t 4 \ --debug \ 2> SRR26957882.fastp.log

# Unpaired if [[ -f SRR26957882.unpaired.trimmed.fastq ]]; then

If it is empty remove it

  if [[ ! -s SRR26957882.unpaired.trimmed.fastq ]]; then
      rm SRR26957882.unpaired.trimmed.fastq
  else
      mv SRR26957882.unpaired.trimmed.fastq SRR26957882.trimmed.unpaired.fastq
      gzip SRR26957882.trimmed.unpaired.fastq
  fi

fi

# R1 if [[ -f SRR26957882.1.trimmed.fastq ]]; then mv SRR26957882.1.trimmed.fastq SRR26957882_1.trimmed.fastq gzip SRR26957882_1.trimmed.fastq fi

# R2 if [[ -f SRR26957882.2.trimmed.fastq ]]; then mv SRR26957882.2.trimmed.fastq SRR26957882_2.trimmed.fastq gzip SRR26957882_2.trimmed.fastq fi

# Discarded: Created if --discard argument is passed if [[ -f SRR26957882.discard.trimmed.fastq ]]; then mv SRR26957882.discard.trimmed.fastq SRR26957882.trimmed.discard.fastq gzip SRR26957882.trimmed.discard.fastq fi

cat <<-END_VERSIONS > versions.yml "NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:FAQCS": faqcs: $(echo $(FaQCs --version 2>&1) | sed 's/^.*Version: //;' ) END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

Work dir: /blue/bphl-mississippi/share/repos/mycosnp-nf/work/4f/d2a76b505d4253274be2b1fbe020df

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

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

We would really appreciate any help or advice that you may have regarding this error.

Thank you.

[zmudge3]

Hi @snallani-msdh ,

Thank you for creating an issue, and apologies for the delay! Would you be able to share the command you used to run the pipeline (either via the command line directly or an HPC submission script)? That will help us debug.

[zmudge3]

We resolved this issue on a call. Here are the steps we took:

• Downgraded Nextflow version to 22.10.6
• Created a tmp folder in the run directory, along with providing the --tmpdir <full_path_to_tmp_folder> in the nextflow run command. Providing the full path to the tmp folder was necessary.