Test example data: No entries found for gene chr16:9000:25001:+ in GFF

[yangchuhua]

To Whom It May Concern,

I downloaded the test data and ran as the example form BAM files, but I got the error: Loaded 0 genes. But the coordinate in GFF3 file locates in the regions in the example -c chr16:+:9000:25000.

I wonder if you have any idea about this error. Do I need to do something for the GFF files?

$ rmats2sashimiplot --b1 ./rmats2sashimiplot_test_data/sample_1_replicate_1.bam,./rmats2sashimiplot_test_data/sample_1_replicate_2.bam,./rmats2sashimiplot_test_data/sample_1_replicate_3.bam --b2 ./rmats2sashimiplot_test_data/sample_2_replicate_1.bam,./rmats2sashimiplot_test_data/sample_2_replicate_2.bam,./rmats2sashimiplot_test_data/sample_2_replicate_3.bam -c chr16:+:9000:25000:./rmats2sashimiplot_test_data/annotation.gff3 --l1 SampleOne --l2 SampleTwo --exon_s 1 --intron_s 5 -o test_coordinate_output

'./rmats2sashimiplot_test_data/sample_1_replicate_1.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_1_replicate_1.bam.bai'
'./rmats2sashimiplot_test_data/sample_1_replicate_2.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_1_replicate_2.bam.bai'
'./rmats2sashimiplot_test_data/sample_1_replicate_3.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_1_replicate_3.bam.bai'
'./rmats2sashimiplot_test_data/sample_2_replicate_1.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_2_replicate_1.bam.bai'
'./rmats2sashimiplot_test_data/sample_2_replicate_2.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_2_replicate_2.bam.bai'
'./rmats2sashimiplot_test_data/sample_2_replicate_3.bam' seems to be indexed already. Please Check out this index file './rmats2sashimiplot_test_data/sample_2_replicate_3.bam.bai'

<module 'misopy' from './miniconda3/envs/sashimiplot_20231109/lib/python2.7/site-packages/MISO/misopy/__init__.pyc'>
Indexing GFF...
  - GFF: ./test_coordinate_output/Sashimi_index/tmp.gff3
  - Outputting to: ./test_coordinate_output/Sashimi_index
WARNING: No entries found for gene chr16:9000:25001:+ in GFF ./test_coordinate_output/Sashimi_index/tmp.gff3
Skipping gene chr16:9000:25001:+...
Loaded 0 genes
  - Loading of genes from GFF took 0.00 seconds
Outputting gene records in GFF format...
  - Output file: ./test_coordinate_output/Sashimi_index/genes.gff
  - Serialization of genes from GFF took 0.01 seconds
Indexing of GFF took 0.01 seconds.
./miniconda3/envs/sashimiplot_20231109/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 "./miniconda3/envs/sashimiplot_20231109/lib/python2.7/site-packages/MISO/misopy/sashimi_plot/sashimi_plot.py", line 293, in <module>
    main()
  File "./miniconda3/envs/sashimiplot_20231109/lib/python2.7/site-packages/MISO/misopy/sashimi_plot/sashimi_plot.py", line 289, in main
    plot_label=plot_label)
  File "./miniconda3/envs/sashimiplot_20231109/lib/python2.7/site-packages/MISO/misopy/sashimi_plot/sashimi_plot.py", line 148, in plot_event
    %(event_name, pickle_dir)
Exception: Event chr16:9000:25001:+ not found in pickled directory ./test_coordinate_output/Sashimi_index. Are you sure this is the right directory for the event?
mv: cannot stat ‘./test_coordinate_output/Sashimi_plot/chr16:9000:25001:+.pdf’: No such file or directory

[EricKutschera]

It looks like you may be running an older version of the code (v2.0.3 or earlier). The test data gff3 uses transcript as the feature name, but v2.0.3 and earlier require the feature to be mRNA: #37

You could try installing the latest version, or you can run from the latest source code using python /path/to/rmats2sashimiplot.py:

git clone https://github.com/Xinglab/rmats2sashimiplot.git
python ./rmats2sashimiplot/src/rmats2sashimiplot/rmats2sashimiplot.py --b1 ...