AUGUSTUS error message: Segmentation fault (core dumped)

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2.2 years 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 • 1.1k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 2.2 years ago by Shin Taguchi ▴ 40

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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 2.2 years ago by lieven.sterck 15k

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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 2.2 years ago by Shin Taguchi ▴ 40

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

ADD REPLY • link 2.2 years ago by Juke34 8.9k

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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 2.2 years ago by Shin Taguchi ▴ 40

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