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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
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stringtie --merge gives error messages #220

Open nozabey opened 5 years ago

nozabey commented 5 years ago

Hi, I tried to merge a couple of gtf files output from stringtie, using stringtie "--merge mode". (I do not have any guide gtf.) However, I got unexpected errors. My command and the error message is as follows.

/home/nozawa/Software/stringtie-master/stringtie --merge \ -o /home/nozawa/Data/alb/HST-STie/albM.gtf \ /home/nozawa/Data/alb/HST-STie/merge_list_M.txt

Error: the input alignment file is not sorted! ./srgtie_merge.sh: line 11: 10796 Segmentation fault (core dumped) /home/nozawa/Software/stringtie-master/stringtie --merge -o /home/nozawa/Data/alb/HST-STie/albM.gtf /home/nozawa/Data/alb/HST-STie/merge_list_M.txt

The content of my merge_list_M.txt is /home/nozawa/Data/alb/HST-STie/LM_wY/albLM_wY.gtf /home/nozawa/Data/alb/HST-STie/PM_wY/albPM_wY.gtf /home/nozawa/Data/alb/HST-STie/WM_wY/albWM_wY.gtf

albM.gtf was generated but seems to have stopped halfway through...

Could someone please give me the way to solve the issue?

gpertea commented 5 years ago

The error message suggests that one of the input GTF files in your merge_list_M.txt might not be sorted properly by chromosome+coordinate, though stringtie should've taken care of that internally. Unfortunately the error message does not clearly specify which file is triggering the problem. I am wondering now if this error wasn't somehow introduced by a recent change in the gff processing code (you are using the very last version of stringtie, right?). Is it possible to share with me the 3 .gtf files you have there in that merge_list_M.txt so I can reproduce and fix the issue?

nozabey commented 5 years ago

Thank you very much for your reply. I have used StringTie v1.3.5. I am attaching the 3 gtf files. Could you please check them? [gtfs.zip]

gpertea commented 5 years ago

Thank you for sending the files, indeed the problem seems to be related to what I thought. I've just released v1.3.6 which should include the fix for this problem - thanks again for helping me identify this issue.

nozabey commented 5 years ago

Thank you very much for your prompt reply and for releasing the new version of the software. I used the version with exactly the same command. The program now works without any error!! Thank you very much! Best regards,

asgar-hussain commented 4 years ago

Hi, I am getting same error when using merge option with version 2.1.3.

gpertea commented 4 years ago

@asgar-hussain can you share an example file (or files) where that option crashes? If it's an input file issue you might be able to trigger a crash even with a single input file -- and then you can share just that file with me.

asgar-hussain commented 4 years ago

I am sharing two gtf files generated with stringtie v_2.1.3 with reference (gencode v33 gtf ). I do not get any errors while using one gtf file at a time but for than one file it gave following error : command : stringtie --merge -G gencode.v33.annotation.gtf -o merge.gtf test1.gtf test2.gtf

Error: the input alignment file is not sorted! Alignments (1) already found for GL000205.2 !

test.zip](https://github.com/gpertea/stringtie/files/4638241/test.zip)

gpertea commented 4 years ago

Ouch, this looks like a regression bug (though not related to the OP in this topic but it's due to a recent change for other reasons). @asgar-hussain thank you for the example files, that clearly exposed the problem and I fixed it. I've just released v2.1.3b with just the fix for this particular bug.

asgar-hussain commented 4 years ago

Thanks, It is working now.