search

EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
Other
317 stars 70 forks source link

HMMER error #332

Closed mesti90 closed 2 months ago

mesti90 commented 2 months ago

defense-finder 1.3.0 aborted with the following error message in defense-finder-tmp/DF_1/hmmer_results/radar_II__rdrA_II.search_hmm.err:

Fatal exception (source file p7_pipeline.c, line 714): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?) Aborted (core dumped)

HMMER version number is 3.4

The file on which it stopped working is attached.

GCA_022437905.1.fna.gz

cryptogenomicon commented 2 months ago

Error message seems self-explanatory. hmmsearch has a length limit of 100K residues for target sequences. Your input is a 560kb DNA sequence. If you want to search long DNA sequences, that's what nhmmer does.

If this is an issue in someone else's pipeline (defense-finder, for example), you may want to report the problem to them. This doesn't appear to be a problem in HMMER.

mesti90 commented 2 months ago

Sorry, I meant to open this issue in the defense-finder pipeline