IOError: truncated file

[deb0612]

Dear sir,
I tried the new version of rmats2sashimiplot.py with the following command:
python "/lab_nas_home_user/Debbie/biotools/cancer/rmats2sashimiplot-3.0.0/src/rmats2sashimiplot/rmats2sashimiplot.py" --b1 b1.124465A5.txt --b2 b2.sample.txt --event-type SE -e SE.MATS.JCEC.txt" --l1 A --l2 B --exon_s 1 --intron_s 1 -o SE_plot

and show the error message

I don't know why the file was truncated ? and the output Sashimi_plot folder was empty.
I think there might be someting wrong with chrX.

[EricKutschera]

The error seems to be saying that pysam is unable to read one of your bam files. Can you run samtools view on each of your bam files?

The output also shows that your bam files are already indexed. That should be fine, but you could try removing those .bai files and letting rmats2sashimiplot regenerate them

[deb0612]

Thanks, I tried to delete the .bai file and regenerated by rmats2sashimiplot.
There is another error.

[EricKutschera]

From the first screenshot it looks like you were using python 2.7 (/home/user/miniconda3/envs/py27). In the second screenshot it looks like you are using python 3.8 (/usr/lib/python3.8). The SyntaxError is about using python 3 to run code meant for python 2 (#83)

The rmats2sashimiplot code is written for python 2, but can be converted to python 3 with https://github.com/Xinglab/rmats2sashimiplot/blob/master/2to3.sh