Segmentation fault on GenerateTranslationProfile

[josuebarrera]

Dear @Alistair-Turcan and @aaronwacholder,

Thank you for creating iRibo! I'd like to use your software to predict actively translated ORFs in a genome, but I stumbled upon a segmentation fault error while running GenerateTranslationProfile. Here is the error:

/var/spool/gridengine/execd/node609/job_scripts/6399019: line 21: 20554 Segmentation fault iRibo --RunMode=GenerateTranslationProfile --Genome=genome.fasta --Riboseq=riboseq.sorted.bam --CandidateORFs=candidate_orfs --Threads=20 --Max_Length=40

The genome assembly is around 200 Mbp in length, while the BAM file is only 3.7 Gb in size. I ran the job using 200 and 400 Gb of RAM, but the run crashes almost instantly so I don't think memory is the issue. Any help would be deeply appreciated.

Best regards, Josué.

[Alistair-Turcan]

Set the Max_Length to be 39, thats the length iRibo can handle up until (and most riboseq is shorter than that).

[josuebarrera]

Dear @Alistair-Turcan,

Thank you very much for the recommendation. The segmentation fault was caused by the Max_Length parameter, so I kept the default value of 35. But now it gives me another obscure error:

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr: __pos (which is 18446744073709551613) > this->size() (which is 1)
Aborted

I ran the code as:

iRibo --RunMode=GenerateTranslationProfile --Genome=genome.fasta --Riboseq=riboseq.sorted.bam --CandidateORFs=candidate_orfs

Maybe I'm doing something wrong?

Best regards, Josué.

[Alistair-Turcan]

Hmm, not sure. I’m actually not a part of this lab anymore and the repo is maintained at CarvunisLab/Iribo on GitHub now. Maybe someone over there can help you. Good luck!

[josuebarrera]

Thank you so much @Alistair-Turcan, I'll go there and ask about the issue! Take care!