local/miso_sashimi.nf uses fixed parameters to visualize genes

[pengxiao78]

Description of the bug

error [nextflow.exception.ProcessFailedException]: Process NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3) terminated
with an error exit status (1)

Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3) terminated with an error exit status (1)

Command executed:

sashimi_plot --plot-event ENSG00000147403 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:
/usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_gr
id module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality inst
ead.
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 ENSG00000147403 not found in pickled directory index. Are you sure this is the right directory for the event?

Command used and terminal output

Relevant files

No response

System information

No response

[akaviaLab]

The problem isn't matpltoblib. The problem seems to be that miso sashimi has a default of three genes it is trying to visualize, defined

rnasplice/nextflow.config

Line 83 in 1d0494a

miso_genes = 'ENSG00000004961, ENSG00000005302, ENSG00000147403'

These three genes are
ENSG00000004961 - mitochondria related gene
ENSG00000005302 - chromatin remodelling gene
ENSG00000147403 - Ribosomal protein

miso_shashimi misses the pickle version files of these genes. I don't know if the pickle is supposed to be generated in each run (and it isn't), or it was supposed to be provided with it.

I think that having a fixed list of genes is a bad idea, even if it worked.

[wongjy2]

Hi! I am also encountering this issue. Have you been able to fix this bug?

[danielhmendoza01]

I ran into this same error and it seems the fix is too add the version the genes. In my case it was:
miso_genes = 'ENSG00000004961.16, ENSG00000005302.19, ENSG00000147403.19'

I found them in the chrX folder inside the index:
./chrX/ENSG00000004961.16.pickle
./chrX/ENSG00000005302.19.pickle
./chrX/ENSG00000147403.19.pickle