rmats2sashimiplot

[eunbi]

Hello all, 

I'm trying to get sashimiplot using rMATS output and sorted bam file (using STAR).

I used rmats2sashimiplot packages, using following code:

 python3 ./src/rmats2sashimiplot/rmats2sashimiplot.py --b1 /path/to/sample1/replicate1.bam,/path/to/sample1/replicate2.bam --b2 /path/to/sample2/replicate1.bam,/path/to/sample2/replicate2.bam -t MXE -e /path/to/rMATS/output/MXE/file.txt --l1 sample1 --l2 sample2 -o /path/to/output

I got the output file including "Sashimi_index/" and severals "Sashimi_index_{Gene}_{event_id}/", but no "Sashimi plot/".

It showed error like:

Indexing '/path/to/sample1/replicate1.bam'.
sh: samtools: command not found
Indexing '/path/to/sample1/replicate1.bam'.
sh: samtools: command not found
Indexing '/path/to/sample1/replicate1.bam'.
sh: samtools: command not found
Indexing '/path/to/sample1/replicate1.bam'.
sh: samtools: command not found
[E::idx_find_and_load] Could not retrieve index file for '/path/to/sample1/replicate1.bam'

  File "/home/ec2-user/rmats2sashimiplot-2.0.4/src/MISO/misopy/index_gff.py", line 77
    print "Making directory: %s" %(chrom_dir)

SyntaxError: invalid syntax
/usr/bin/python3 /home/ec2-user/rmats2sashimiplot-2.0.4/src/MISO/misopy/sashimi_plot/sashimi_plot.py --plot-event "chrX:159327208:159327330:+@chrX:159332171:159332266:+@chrX:159335709:159335816:+@chrX:159337297:159337375:+" /home/ec2-user/eunbi/sashimi/Sashimi_index_Phka2_1 /home/ec2-user/eunbi/sashimi/Sashimi_index_Phka2_1/sashimi_plot_settings.txt --output-dir /home/ec2-user/eunbi/sashimi/Sashimi_plot
  File "/home/ec2-user/rmats2sashimiplot-2.0.4/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 " \)?
mv: cannot stat ‘/home/ec2-user/eunbi/sashimi/Sashimi_plot/chrX:159327208:159327330:+@chrX:159332171:159332266:+@chrX:159335709:159335816:+@chrX:159337297:159337375:+.pdf’: No such file or directory
  File "/home/ec2-user/rmats2sashimiplot-2.0.4/src/MISO/misopy/index_gff.py", line 77
    print "Making directory: %s" %(chrom_dir)
                               ^

I'm sorry I have no idea what can I do next.

Can anybody help? 

Thanks,

Eunbi

[kutsc...@gmail.com]

Those syntax errors are likely from running rmats2sashimiplot with python3 without first running 2to3.sh: https://github.com/Xinglab/rmats2sashimiplot/tree/v2.0.4#dependencies

This post about running 2to3.sh might help: https://github.com/Xinglab/rmats2sashimiplot/issues/75

Also you have errors like: "sh: samtools: command not found" which could happen if samtools is not installed or else not on your $PATH

Eric