Directory not found universc

[HafsaKM]

Hi! Quite new to this, I am trying to run the scrna-seq pipline and I keep running into this error. I just wanted to run this piepline with the universc alignment tool on a small test.

This is the shell script I used

#!/bin/bash
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=16:mem=64gb

module load tools/prod
module load Nextflow/23.10.0

nextflow run nf-core/scrnaseq \
  --input /rds/general/user/hk1723/home/test_files/sample_sheet.csv \
  --outdir /rds/general/user/hk1723/home/test_files/results \
  --genome GRCh38 \
  --aligner universc \
  -profile singularity \

This was in the execution report file

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC (SRR12842503)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC (SRR12842503)` terminated with an error exit status (1)

Command executed:

  universc \
      --id 'sample-SRR12842503' \
      -R1 SRR12842503_S1_L001_R1_001.fastq.gz -R2 SRR12842503_S1_L001_R2_001.fastq.gz \
      --technology '10x' \
      --chemistry 'auto' \
      --reference cellranger_reference \
      --description SRR12842503 \
      --jobmode "local" \
      --localcores 6 \
      --localmem 36 \
      --per-cell-data \
       1> _log 2> _err
  
  # save log files
  echo !! > sample-SRR12842503/outs/_invocation
  cp _log sample-SRR12842503/outs/_log
  cp _err sample-SRR12842503/outs/_err
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC":
      cellranger:  $(echo $(cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* //g' | sed 's/(//g' | sed 's/)//g' ))
      universc:  $(echo $(bash /universc/launch_universc.sh --version | grep version | grep universc  | sed 's/^.* //g' ))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 16: sample-SRR12842503/outs/_invocation: No such file or directory

Work dir:
  /var/tmp/pbs.9327528.pbs/work/65/67e2dbe50ffbc20f8701c774d19c1c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

The directory it says it couldn't find, I thought that would be created by an internal program, not sure why it hasn't been created? Thanks so much for your answers!