rMATS keeps running but no outputs nor any errors reported

Question

[Yingzi Zhang]

Dear all,

I was using rMATS to do alternative splicing analysis.

My command is like this:

python $rMATS/rmats.py --b1 ko.txt --b2 wt.txt --gtf ./GCF_000001405.39_GRCh38.p13_genomic.gtf --od ./rMATS -t paired --readLength 150 --cstat 0.0001 --nthread 1 --libType fr-secondstrand

It keeps running but no outputs nor any errors reported.

I searched to try to find an answer and found this. I checked and believed the indexes being used are okay.

Does anyone know how to solve this? Or does rMATS doesn't give outputs until it finishes all its processes? Thank you.

Regards,

Yingzi

Answer 1

[Yingzi Zhang]

In my case, I later found that it would suddenly give all the outputs after it completed its processes. I hope this would help if you meet a similar situation. Thank you.

Best, Yingzi