HMMSCAN error in batch submission
0
0
Entering edit mode
20 months ago

Hi there,

I have several genomes fasta files for screening based on HMM. I wrote this very simple script. It seems that works - the output files are right. However, I also got this message

"Incorrect number of command line arguments. Usage: hmmscan [-options] <hmmdb> <seqfile>

where most common options are: -h : show brief help on version and usage

To see more help on available options, do /Users/alexjones/miniconda3/bin/hmmscan -h"

Someone knows why I get this message? The script is wrong?

I appreciate any tips. Thanks.

for file in ./*.fasta;
do
  hmmscan --domtblout ${file}.out.dm Target_HMM.txt ${file} > ${file}.out;
done
bash HMM script • 469 views
ADD COMMENT

Login before adding your answer.

Traffic: 1853 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6