Trying to use hmmer to search genes over metagenome assembled genomes

Trying to use hmmer to search genes over metagenome assembled genomes

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Hello I have a hmm file (my genes.hmm) that I want to use to search some genes over some MAGs that I elaborated. For this purpose I installed hmmer and tried to run hmmsearch as the following:

First I converted he nucleotide sequences of my MAGs into aminoacidic sequences

transeq -sequence MAG1.fasta -outseq MAG1.faa

After that I ran the hmmsearch program

hmmsearch --cpu 9 --tblout genes_table.txt mygenes.hmm MAG1.faa > genes_results.txt

But I got an error message:

Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?)

It seems hmmer cannot deal with sequences greater than 100K aminoacids. I took a look to my MAG to see if there was an aminoacidic sequence greater than 100K aminoacids and there were more than one with a length over 100k.

So hmmer cannot deal with sequences larger than 100K aminoacids ? Is there a way to handle this ?

thanks for your time.

Valentín.


MAGs


genes


hmmer

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