Question: rMATS 4.0.2 (turbo) error when running the statistical part
0
gravatar for Ivó Hernández Hernández
8 months ago by
Spain/Madrid/CBMSO

Hello everybody!!!

I'm getting an error while running the latest version of rMATS (4.0.2 turbo) when the program reaches the statistical analysis part. I here show you the command-line order I used and the hole output till the error. I hope you can help me with this issue. Thanks a lot in advance.

#

rmats.py --b1 b1.txt --b2 b2.txt -t paired --gtf Mus_musculus.GRCm38.94.gtf --readLength 76 --cstat 0.0001 --nthread 10 --od bam_test

There are 54532 distinct gene ID in the gtf file There are 137862 distinct transcript ID in the gtf file There are 34135 one-transcript genes in the gtf file There are 813724 exons in the gtf file There are 26209 one-exon transcripts in the gtf file There are 21399 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.528094 Average number of exons per transcript is 5.902453 Average number of exons per transcript excluding one-exon tx is 7.053236 Average number of gene per geneGroup is 7.390554

#

Done processing each gene from dictionary to compile AS events

Found 19119 exon skipping events Found 920 exon MX events

Found 8038 alt SS events

There are 5128 alt 3 SS events and 2910 alt 5 SS events.

Found 3868 RI events

#

Running the statistical part.

Traceback (most recent call last):

File "/home/olivo/miniconda2/envs/rMATS/bin/rmats.py", line 308, in <module> main()

File "/home/olivo/miniconda2/envs/rMATS/bin/rmats.py", line 289, in main run_stat(jc_it % ('SE'), args.tstat, 'JC', 'SE', args.cstat, args.od, args.tmp, args.stat)

File "/home/olivo/miniconda2/envs/rMATS/bin/rmats.py", line 254, in run_stat call(map(str, [rmats_c, '-i', istat, '-t', tstat, '-o', ostat % ('P-V'), '-c', cstat,]), stdout=FNULL)

File "/home/olivo/miniconda2/envs/rMATS/lib/python2.7/subprocess.py", line 172, in call return Popen(popenargs, *kwargs).wait()

File "/home/olivo/miniconda2/envs/rMATS/lib/python2.7/subprocess.py", line 394, in __init__ errread, errwrite)

File "/home/olivo/miniconda2/envs/rMATS/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception

OSError: [Errno 2] No such file or directory

ADD COMMENTlink modified 8 months ago • written 8 months ago by Ivó Hernández Hernández10
1
gravatar for Ivó Hernández Hernández
8 months ago by
Spain/Madrid/CBMSO

Hi everybody.

I solved the problem by explicitly specifying the version of python to run rmats.py (python2.7 rmats.py ..). This puzzles me as I created a specific conda environment for rMATS with python version 2.7. It now works properly.

Later I found this site: https://github.com/bioconda/bioconda-recipes/issues/12782

It seemed to be a problem with the installation of rMATS through conda that has already been solved, so the solution now is to reinstall.

conda install -c bioconda rmats

ADD COMMENTlink written 8 months ago by Ivó Hernández Hernández10
0
gravatar for Jeremy Leipzig
8 months ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

try specifying a --tmp directory

ADD COMMENTlink written 8 months ago by Jeremy Leipzig18k
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