Nextflow workflow report

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_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)'

Caused by:
  Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)` terminated with an error exit status (1)


Command executed:

  sashimi_plot --plot-event ENSG00000004961 index miso_settings.txt --output-dir sashimi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
      python: $(python --version | sed "s/Python //g")
      misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').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
  /usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
    warnings.warn(message, mplDeprecation, stacklevel=1)
  Traceback (most recent call last):
    File "/usr/local/bin/sashimi_plot", line 11, in 
      sys.exit(main())
    File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
      plot_label=plot_label)
    File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 142, in plot_event
      %(event_name, pickle_dir)
  Exception: Event ENSG00000004961 not found in pickled directory /gscratch/scrubbed/srlab/nxf.YhOyO1QXyw/index. Are you sure this is the right directory for the event?

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20251205_rnasplice_Ptua/work/92/3394e40f19f8f80b27fcba3541972e

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-misopy-0.5.4--py27h9801fc8_5.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`