nf-core/rnasplice

sashimi_plot error

Closed this issue · 2 comments

Description of the bug

I'm getting an error message when running rnasplice about the sashimi_plot. The error message is copied below:

-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3)'

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_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 ENSG00000147403 not found in pickled directory index. Are you sure this is the right directory for the event?

Command used and terminal output

This is the command I ran:
nextflow run nf-core/rnasplice -profile docker -params-file params.yaml

This was my params.yaml file:
input: '/path/samplesheet.csv'
contrasts: '/path/contrastsheet.csv'
outdir: '/path/outdir/'
source: 'fastq'
genome: 'BDGP6'
aligner: 'star_salmon'
save_reference: true
dexseq_dtu: true
min_samps_gene_expr: 6
min_gene_expr: 10
min_samps_feature_expr: 3
min_feature_expr: 10
min_samps_feature_prop: 3
min_feature_prop: 0.1

This was my Contrastsheet:
contrast,treatment,control
AUB_CS,AUB,CS

Relevant files

No response

System information

Nextflow version: version 23.10.0
Linux OS
Version of nf-core/rnasplice 1.0.1

Hey @GimenaA

The default gene identifier in the config is an example of a gene from the human genome. You are using a Drosophila melanogaster genome, therefore please provide a gene found in that genome.

Thanks,
James

Thank you!