Error when running on rMATS generated BAM files

[nicholas-moskwa]

Hi,

I am trying to generate sashimi plots using BAM files made from running rMATS on FASTQ files. I am using two files that hold my replicates.

My run: python /Packages/rmats2sashimiplot/src/rmats2sashimiplot/rmats2sashimiplot.py --b1 10_129S.txt --b2 10_B6.txt -c chr7:+:27256438:27284145:/genomes/mm10/gencode.vM36.annotation.gff3 --l1 129S --l2 B6 --exon_s 1 --intron_s 5 -o ${dir_out}

My error: File "/Packages/rmats2sashimiplot/src/MISO/misopy/index_gff.py", line 77 print "Making directory: %s" %(chrom_dir) ^ SyntaxError: invalid syntax File "/Packages/rmats2sashimiplot/src/MISO/misopy/sashimi_plot/sashimi_plot.py", line 46 print "WARNING: %s does not end in .miso_bf, are you sure it is the " \ ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("WARNING: %s does not end in .miso_bf, are you sure it is the " )? '/mm10-tmp/2024-02-01-13_40_35_331660_bam1_1/Aligned.sortedByCoord.out.bam' is indexed already: '/mm10-tmp/2024-02-01-13_40_35_331660_bam1_1/Aligned.sortedByCoord.out.bam.bai' 'mm10-tmp/2024-02-01-13_40_35_331660_bam2_1/Aligned.sortedByCoord.out.bam' is indexed already: '/mm10-tmp/2024-02-01-13_40_35_331660_bam2_1/Aligned.sortedByCoord.out.bam.bai'

Thanks for your help!

[EricKutschera]

Here's a similar issue: https://github.com/Xinglab/rmats2sashimiplot/issues/138#issuecomment-2454752015

You could try:

cd /Packages/rmats2sashimiplot
./2to3.sh

[nicholas-moskwa]

Okay, that changed the error, I think most of the script ran, but now I see this error:

Exception: Event 7_2725643827284146- not found in pickled directory /pod/2/ch-lee-lab/labdata/moskwn/RNA-seq/RMT0015/10_Rmats2sashimiplot/Sashimi_index. Are you sure this is the right directory for the event?

Does rmatsashimiplot only plot events that show up in rMATS?

[EricKutschera]

That error can happen if you use the same -o directory for multiple runs. The code will see files from a previous run (which may have had an error) and the old files can cause the error: https://github.com/Xinglab/rmats2sashimiplot/issues/92#issuecomment-1446841032