empty output file after running rmats

[Behzad Moumbeini]

Hi everybody,

I am using rmats for the alternative splicing analysis (using fastq files and hg38) using the following command:

 rmats.py --s1 s1.txt --s2 s2.txt --gtf gencode.v39.annotation.gtf  --bi /STAR/hg38/ -t paired --readLength 150 --nthread 4 --novelSS --mil 50 --mel 500 --od /output/ --tmp /tmp_output/

During the analysis everything was OK and at the end I got the following message:

ase: 3.570340871810913

count: 0.5707430839538574

Processing count files.

Done processing count files.

Showing the analysis was finished successfully.

I tried the command with and without “--novelSS --mil 50 --mel 500 ” and have the same problem. 

In the output I have a lot of resulting files. the following files have many rows:

fromGTF.A3SS.txt

fromGTF.A5SS.txt

fromGTF.MXE.txt

fromGTF.RI.txt

fromGTF.SE.txt

But the rest of files only have headers in fact they do not have any rows!!!

Summary.txt also looks like this:

EventType TotalEventsJC TotalEventsJCEC SignificantEventsJC SigEventsJCSample1HigherInclusion SigEventsJCSample2HigherInclusion SignificantEventsJCEC SigEventsJCECSample1HigherInclusion SigEventsJCECSample2HigherInclusion

SE 0 0 0 0 0 0 0 0

A5SS 0 0 0 0 0 0 0 0

A3SS 0 0 0 0 0 0 0 0

MXE 0 0 0 0 0 0 0 0

RI 0 0 0 0 0 0 0 0

If I use bam file instead of fastq files (different command with b1.txt and b2.txt)

Since I did not get any error or log file, I do not know what the problem is. does any one has experience ? Or do you know what problem could be?

[kutsc...@gmail.com]

The read outcomes printed when running rmats can usually show a reason for seeing only headers in the output files like in this post: https://github.com/Xinglab/rmats-turbo/issues/149

Eric