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mdmparis / defense-finder

Systematic search of all known anti-phage systems.
GNU General Public License v3.0
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[BUG] Hmmer error #66

Open mesti90 opened 2 months ago

mesti90 commented 2 months ago

I called defense-finder run -o Typifier_results/Defensefinder_output/GCA_022437905.1_defensefinder -w 1 Intermediate_files/Genomes/GCA_022437905.1.fna

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

mesti90 commented 2 months ago

I managed to "solve" this problem by commenting out line 714 from hmmer p7_pipeline.c, but probably it's a suboptimal solution. I recommend to determine in the defense-finder scripts if hmmer could me run for the given sequence and return an error message if not.

jeanrjc commented 1 week ago

Hello,

Your sequence is not detected as a nucleotide fasta file by pyhmmer, so it continues as if your sequence was a protein fasta file with 1 protein. Maybe check your sequence, or ask to pyhmmer why it does not consider it as DNA sequence (it considers it's ambiguous).

We could stop when its ambiguous to prevent this though.