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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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Hmmbuild segmentation failure #293

Closed spiceeeheu closed 1 year ago

spiceeeheu commented 1 year ago

Hi, I am trying to build a profile with my sequence files and I face input failure. Alignment input open failed. /cm/local/apps/slurm/var/spool/job112730/slurm_script: line 14: 29906 Segmentation fault hmmbuild 350_fq1.hmm /storage/homes/jiatongh/anvio/350_fq1.fq

I am not really sure what is wrong (or my input file format was wrong), I ran it on a linux ssh and the assigned memory is 1gb. My fq is forward sequence that is roughly 10 gb. I would really appreciate any help! Thanks

cryptogenomicon commented 1 year ago

I'm not sure what you're trying to do here, but you might want to start with the tutorial in the User's Guide to learn more about how HMMER works and what it's for.

I'm guessing that your input .fq file is a 10G FASTQ file of reads, but HMMER hmmbuild is expecting to get a multiple sequence alignment of a particular sequence family that you want to make a profile HMM of, not a FASTQ read file.