AUGUSTUS error message: Segmentation fault (core dumped)

0

Entering edit mode

19 months ago

Shin Taguchi ▴ 40

Hi, everyone.

I am attempting to make a gene prediction using AUGUSTUS. For practice, I tried to perform a gene prediction on publicly available sequence data a fly, referencing Drosophila melanogaster data.

augustus --species=fly sequence.fasta > augustus.test.gff

Then I got the following error message.

Segmentation fault (core dumped)

Could you tell me how to solve this problem?

augustus gene-prediction • 876 views

ADD COMMENT • link updated 19 months ago by Ram 43k • written 19 months ago by Shin Taguchi ▴ 40

1

Entering edit mode

hard to tell without more info but my best guess would be it's running out of memory. So run this job with more memory (or on a machine with more memory)

ADD REPLY • link 19 months ago by lieven.sterck 15k

0

Entering edit mode

lieven.sterck

Hi.

Thank you for your advice. My PC has 128GB of total memory and I don't have any other jobs running in parallel. Does gene prediction by AUGUSTUS use that much memory?

ADD REPLY • link 19 months ago by Shin Taguchi ▴ 40

0

Entering edit mode

What version of Augustus do you use and how did you install it?

ADD REPLY • link 19 months ago by Juke34 8.5k

0

Entering edit mode

I installed version 3.2.2 from Bioconda. However, when I used version 3.4.0 through the Singularity container, this error was resolved. Thank you very much.

ADD REPLY • link 19 months ago by Shin Taguchi ▴ 40

Login before adding your answer.