Error running the rMATS for splicings

Question

[Omics data mining]

Dear all,

I am working on RNASEQ data and running RNASeq-MATS.py to get alternative splicing by just doing comparision among 2 samples.

python rMATS.3.2.5/RNASeq-MATS.py -b1 s1.bam -b2 s2.bam  -gtf  sample.gtf   -o bam_test -t paired -len 100 -a 8 -c 0.0001 -analysis U -novelSS 1 -keepTemp

error detail :

 done indexing bam files..
start getting AS events from GTF and BAM files

getting AS events function..

 getting AS events is done with status 256
 error in getting AS events 256

 error detail: Traceback (most recent call last):

  File "rMATS.3.2.5/bin/processGTF.BAMs.py", line 40, in <module>
    filemode='w')
  File "/usr/lib/python2.7/logging/__init__.py", line 1540, in basicConfig
    hdlr = FileHandler(filename, mode)
  File "/usr/lib/python2.7/logging/__init__.py", line 911, in __init__
    StreamHandler.__init__(self, self._open())
  File "/usr/lib/python2.7/logging/__init__.py", line 936, in _open
    stream = open(self.baseFilename, self.mode)
IOError: [Errno 2] No such file or directory: rMATS.3.2.5/1/log.process.GTF.SAMs.3.2.5.2018-07-05 12:51:00.645204'
2018-07-05 12:51:00,841 There is an exception in getting AS events
2018-07-05 12:51:00,841 Exception: <type 'exceptions.Exception'>
2018-07-05 12:51:00,841 Detail:

To fix it ,

• I crossed check my GTF file and BAM files. Validated BAM files with picard tools which indicated no issues in my BAM files.

• Also, I converted gff3 to gtf using gffread with default paramters
  and used as input.

Can anybody suggest me how to fix this error ???

Thanks Archana

[Bastien Hervé]

My hint is that the script can't find the good log path. In your case rMATS.3.2.5/1/

In the rMATS.3.2.5 script it's written that the temp file results from the concatenation of the -o option + /temp

Something goes wrong and I guess that the script took the -novelSS value (so here, 1) as output directory

When I read your command line I see multiple space in it, retry like this please :

python rMATS.3.2.5/RNASeq-MATS.py -b1 s1.bam -b2 s2.bam -gtf sample.gtf -o bam_test -t paired -len 100 -a 8 -c 0.0001 -analysis U -novelSS 1 -keepTemp

[WouterDeCoster]

Taking a look at the code is painful:

https://github.com/CBIIT/mats-nih/blob/master/3.0.9/RNASeq-MATS.py#L134

Should have used argparse

Almost makes me want to open a PR, but then again, I should be writing my thesis.

[Bastien Hervé]

Plus, the last version is not on Github, I downloaded it via sourgeforge then I took a look...

[Kevin Blighe]

I'm not sure that you're running it correctly. Please take a look at my answer here: A: input for rMATS

The inputs should be text files that merely list your BAM files.

Also, be aware that [bizarrely] rMats requires that your BAMs contains reads that are each the same length.

[WouterDeCoster]

Medhat and I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: