Hi, I am currently running for the first time the #C0493FQQZ3P pipeline and encounter the attached issue. The group assignment seems to be performed correctly, however I believe the issue is related to the "+++" attached to

--groups 1-6,7-9+++

. Did anybody face a similar issue?

Caused by:
  Process `NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (TREATMENT-CONTROL)` terminated with an error exit status (1)


Command executed:

  suppa.py \
          clusterEvents \
          --dpsi TREATMENT-CONTROL_transcript_diffsplice.dpsi \
          --psivec TREATMENT-CONTROL_transcript_diffsplice.psivec \
          --dpsi-threshold 0.05 \
          --eps 0.05 \
          --metric euclidean \
          --min-pts 20 \
          --groups 1-6,7-9+++ STATS %CPU=563 TIME=0 I/O=1500699 212 318 13 0 0
  PID   USER     TIME  COMMAND
      1 USER  0:00 sinit
     12 USER  0:00 /bin/bash -c cd XXX/nxf_work/analysis/f2/fc387527be25b47b90783ee353f50b; eval export PYTHONNOUSERSITE="1" export R_PROFILE_USER="/.Rprofile" export R_ENVIRON_USER="/.Renviron" export JULIA_DEPOT_PATH="/usr/local/share/julia" export PATH="$PATH:XXX/nxf_pipelines/nf-core-rnasplice_1.0.4/1_0_4/bin"; /bin/bash XXX/nxf_work/analysis/f2/fc387527be25b47b90783ee353f50b/.command.run nxf_trace
     13 USER  0:00 /bin/bash XXX/nxf_work/analysis/f2/fc387527be25b47b90783ee353f50b/.command.run nxf_trace
     37 USER  0:00 /bin/bash XXX/nxf_work/analysis/f2/fc387527be25b47b90783ee353f50b/.command.run nxf_trace
     55 USER  0:00 ps fx
  ++ stat mem=35 0 0 0 0 0 0 0
  ++ stat SUM=0 0 0 0 0 0 0 0
  ++ stat PEAK=0 0 0 0 0 0 0 0

   \
          --clustering DBSCAN \
            -o TREATMENT-CONTROL_transcript_cluster

      cat <<-END_VERSIONS > versions.yml
      "NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI":
          suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)")
      END_VERSIONS

Command exit status:
  1

Command output:
  PID   USER     COMMAND
      1 USER sinit
     15 USER /bin/bash -c cd XXX/nxf_work/analysis/e2/ab8aad961b90324cc160972dd60132; eval export PYTHONNOUSERSITE="1" export R_PROFILE_USER="/.Rprofile" export R_ENVIRON_USER="/.Renviron" export JULIA_DEPOT_PATH="/usr/local/share/julia" export PATH="$PATH:XXX/nxf_pipelines/nf-core-rnasplice_1.0.4/1_0_4/bin"; /bin/bash .command.run nxf_trace
     16 USER /bin/bash .command.run nxf_trace
     37 USER /bin/bash -euo pipefail .command.sh
     39 USER /bin/bash .command.run nxf_trace
     45 USER {suppa.py} /usr/local/bin/python /usr/local/bin/suppa.py clusterEvents --dpsi TREATMENT-CONTROL_transcript_diffsplice.dpsi --psivec TREATMENT-CONTROL_transcript_diffsplice.psivec --dpsi-threshold 0.05 --eps 0.05 --metric euclidean --min-pts 20 --groups 1-6,7-9+++ STATS %CPU=563 TIME=0 I/O=1500699 212 318 13 0 0
     46 USER ps fx
  ++ stat mem=37 0 11288 1268 11292 1268 3 1
  ++ stat mem=45 0 213812 43044 213812 46156 0 2
  ++ stat SUM=0 0 225100 44312 225104 47424 3 3
  ++ stat PEAK=0 0 225100 44312 225104 47424 3 3

  ++ stat mem=37 0 11288 1268 11292 1268 3 1
  ++ stat mem=45 0 465196 69320 465196 70288 1 3
  ++ stat SUM=0 0 476484 70588 476488 71556 4 4
  ++ stat PEAK=0 0 476484 70588 476488 71556 4 4

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /tmp/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  ERROR:__main__:Unknown error: (<class 'ValueError'>, ValueError("invalid literal for int() with base 10: '9+++'",), <traceback object at 0x2b7d32e34648>)
  INFO:    Cleaning up image...

Work dir:
  XXX/nxf_work/analysis/e2/ab8aad961b90324cc160972dd60132

Container:
  XXX/.singularity/depot.galaxyproject.org-singularity-suppa-2.3--py36_0.img

I have not seen this error before, but I know that the pipeline is very sensitive toward the naming of things in the contrast sheet (and by extension the sample sheet) -- I would avoid anything that is not a letter or number.

Thanks for your input @Thomas Danhorn! My contrast sheet has the following structure: contrast,treatment,control CTRL_TREATMENT,TREATMENT,CONTROL The sample sheet contains sample names like: CONTROL_REP1, CONTROL_REP2, CONTROL_REP3, TREATMENT_REP1, TREATMENT_REP2 etc. up to TREATMENT_REP6 So, I assume it's not related to the naming in the sample and contrast sheet.

Yes, that should work for SUPPA (

.

would have been problematic, and the

_

in the contrast name can cause issues with other tool, I think, but should be OK for SUPPA). So the line in the script is

--groups 1-6,7-9+++ STATS %CPU=563 TIME=0 I/O=1500699 212 318 13 0 0

, followed by what looks like output from

ps

. None of the stuff after the

7-9

makes any sense in this context, so this is some garbage (starting with

+++

) that got injected into that

.command.sh

somehow. I see two possibilities: The pipeline causes this through some bug (does not seem extremely likely, but you could try an older version to test), or there was some glitch in your system (corrupted RAM or disk?), in which case a rerun should have a decent chance of succeeding. So I would say, run it again (maybe even with

-resume

) and see if you get the same error again (in which case it is not a random glitch).