Error checking bam files

[RaghdaKailany]

Hi, I am trying to use rmats2sashimiplot using the bam files but I am getting this error can you please tell me what I am doing wrong ?

Thanks in advance

(base) raghdakailany@raghdas-air rmats2sashimiplot % python rmats2sashimiplot.py --b1 \ ../Users/raghdakailany/Desktop/nep_data/wm/wm1.bam,\ ../Users/raghdakailany/Desktop/nep_data/wm/wm2.bam,\ ../Users/raghdakailany/Desktop/nep_data/wm/wm3.bam --b2 \ ../Users/raghdakailany/Desktop/nep_data/67m/67m1.bam,\ ../Users/raghdakailany/Desktop/nep_data/67m/67m2.bam,\ ../Users/raghdakailany/Desktop/nep_data/67m/67m3.bam \ -c chr3L:+:19794898:19796392:..//Users/raghdakailany/Desktop/nep_data/dmel-all-r6.56.gtf \ --l1 SampleOne --l2 SampleTwo --exon_s 1 --intron_s 5 \ -o test_coordinate_output

usage: rmats2sashimiplot [-h] -o OUT_DIR [--l1 L1] [--l2 L2] [--event-type {SE,A5SS,A3SS,MXE,RI}] [-e EVENTS_FILE] [-c COORDINATE]
[--s1 S1] [--s2 S2] [--b1 B1] [--b2 B2] [--exon_s EXON_S] [--intron_s INTRON_S] [--group-info GROUP_INFO]
[--min-counts MIN_COUNTS] [--color COLOR] [--font-size FONT_SIZE] [--fig-height FIG_HEIGHT]
[--fig-width FIG_WIDTH] [--hide-number] [--no-text-background] [--keep-event-chr-prefix]
[--remove-event-chr-prefix]
rmats2sashimiplot: error: Error checking bam files given as --b1: ../Users/raghdakailany/Desktop/nep_data/wm/wm1.bam is not a file

[EricKutschera]

These are the lines for the error:
https://github.com/Xinglab/rmats2sashimiplot/blob/v3.0.0/src/rmats2sashimiplot/rmats2sashimiplot.py#L129
https://github.com/Xinglab/rmats2sashimiplot/blob/v3.0.0/src/rmats2sashimiplot/rmats2sashimiplot.py#L62

It looks like you ran the command from rmats2sashimiplot/src/rmats2sashiplot/. The ../ from ../Users/raghdakailany/Desktop/nep_data/wm/wm1.bam would be rmats2sashimiplot/src. Are your bam files actually in that directory?