Question: Error running the rMATS for splicings
0
gravatar for archie
8 months ago by
archie70
India
archie70 wrote:

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

rna-seq ngs rmats • 557 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 8 months ago by archie70
1

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
ADD REPLYlink modified 8 months ago • written 8 months ago by Bastien Hervé3.7k
1

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.

ADD REPLYlink written 8 months ago by WouterDeCoster37k

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

ADD REPLYlink written 8 months ago by Bastien Hervé3.7k

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.

ADD REPLYlink written 8 months ago by Kevin Blighe39k

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:

101010 Button

ADD REPLYlink written 8 months ago by WouterDeCoster37k
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