segmentation fault error (core dumped) aborted

[Waqasuddin Khan]

Hi Community,

I am running FIMO:

fimo --oc /home/regmwkh/Scratch/databases_work/vcf_data/fimo_output --verbosity 1 --bgfile my.fna.bfile --thresh 1.0E-4 HOCOMOCOv9.meme my.fasta

but I got the segmentation fault error.

When I just take only 5 sequences from my fasta file to run, FIMO works well. But for ~0.4 million sequences, FIMO aborted.

Any help appreciated.

Thanks,

Waqas.

[CharlesEGrant]

Hi Waqas,

Which version of FIMO are you running?

Would it be possible to forward us a copy of the my.fasta file? That would help us troubleshoot the problem.

Charles

[Waqasuddin Khan]

Hi Charles,

FIMO version is 4.11.1. Here, I am attaching my.fasta. (Charles attachment is at your gmail ID)

 

Looking forward for your kind response.

Thanks,

Waqas.

[CharlesEGrant]

Hi Waqas,

Some of the headers for your sequences are over 1000 characters long. See, for example, the sequence at line 491845. The longest sequence header that FIMO can accommodate is 512 characters. FIMO should be catching this and producing a sensible error message, we'll see that this is fixed in the next release. In the meantime you'll need to make sure your sequence headers are less than 512 characters long.

Charles