.command.sh: line 4: rmats.py: command not found

[angarb]

Problem

Pipeline (master branch) is failing at rMATS step.

Error executing process > 'rmats (human_test gencode)'
Caused by:
 Process `rmats (human_test gencode)` terminated with an error exit status (127)
Command executed:
 echo SRR1039512.Aligned.sortedByCoord.out.bam,SRR1039517.Aligned.sortedByCoord.out.bam,SRR1039516.Aligned.sortedByCoord.out.bam > b1.txt
 rmats.py     --b1 b1.txt     --gtf gencode.v32.primary_assembly.annotation.gtf     --od ./     --tmp tmp     --libType fr-firststrand     -t paired     --nthread 30     --readLength 60     --mil 50     --mel 500 --variable-read-length --statoff  --allow-clipping
 rmats_config="config_for_rmats_and_postprocessing.txt"
 echo b1 b1.txt > $rmats_config
 echo rmats_gtf    gencode.v32.primary_assembly.annotation.gtf >> $rmats_config
 echo ref_gtf     gencode.v32.primary_assembly.annotation.gtf >> $rmats_config
 echo fasta      GRCh38 >> $rmats_config
 echo reads      paired >> $rmats_config
 echo readlen     60 >> $rmats_config
 echo rmats_id    human_test >> $rmats_config
 LU_postprocessing.R
 # save .command.* logs
 task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash
Command exit status:
 127
Command output:
 (empty)
Command error:
 .command.sh: line 4: rmats.py: command not found
Work dir:
 /projects/anczukow-lab/gudurg/work/7d/6ff5aceeca6dc479703b3de870906d

Should be able to replicate with: sbatch /projects/anczukow-lab/splicing_pipeline/splicing-pipelines-nf/examples/human_test/human_test_main.pbs

Java Edition: openjdk version "17.0.2" 2022-01-18 OpenJDK Runtime Environment (build 17.0.2+8-86) OpenJDK 64-Bit Server VM (build 17.0.2+8-86, mixed mode, sharing)

Nextflow Edition: version 22.10.5 build 5840 created 14-01-2023 13:42 UTC (08:42 EDT) cite doi:10.1038/nbt.3820

This error was reproduced by @Gayathri-Guduru and @angarb on Sumner.

Solution

Implementation

[angarb]

@cgpu

[cgpu]

@cgpu

thank you @angarb, looking into it. As we discussed, since there has been an update in your HPC of the Nextflow version, could you check which one is the new version with nextflow -v.

Once we know which the version is, I will add it in our continuous integration testing file here https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/master/.github/workflows/ci.yml#L11

This will show us if the issue is reproducible with this particular Nextflow version outside of your HPC environment, and will guide our debugging efforts either towards the Nextflow version or other.

[marina-yurieva]

N E X T F L O W version 22.12.0-edge build 5830 created 13-12-2022 21:22 UTC (16:22 EDT) cite doi:10.1038/nbt.3820 http://nextflow.io