Hmmer scan eror

Question

[slin023]

Hello, I am new to bioinformatics. I recently used hmmer to search homolog of transcript. I used hmmer 3.1b2 on SLURM. Here is the script I used:

##!/bin/bash
##SBATCH --qos pq_mdegenna
##SBATCH --account iacc_mdegenna
##SBATCH -n 16
##SBATCH -N 1
##SBATCH --mem 25000
##SBATCH --output=log

module load hmmer/3.1b2

##Running HMMER to identify protein domains
hmmscan --cpu 16 --domtblout /scratch/slin023/trinotate/Pfam-A.hmm /scratch/slin023/PhormiaCodingRegion/Phormia_de_novo_transcriptome_assembly_V1.fasta.transdecoder.pep > pfam.log

However, the data cannot be processed, so I check the Pfam.log, it shows `Incorrect number of command line arguments.

Usage: hmmscan [-options] <hmmdb> <seqfile>`

I also check the log file, it shows

profiling:/home/software/hmmer/hmmer-3.1b2/src/hmmscan.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/errors.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/hmmer.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/logsum.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/mpisupport.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_bg.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_hmm.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_hmmfile.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_pipeline.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_profile.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_tophits.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_trace.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/p7_scoredata.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/fm_general.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/fm_sse.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/fm_ssv.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/impl_sse/fwdback.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/impl_sse/io.gcda:Cannot open
profiling:/home/software/hmmer/hmmer-3.1b2/src/impl_sse/msvfilter.gcda:Cannot open

Here are the list of troubleshooting I did so far, but nothing works:

• I hmmerpress the Pfam-A.hmm before
• I also checked the Pfamm-A.hmm version with the hmmer version I used, they are all 3.1b2

Does anyone have any clues what is going on and if there is anything wrong with my script. Thank you for your time and your patience.

Answer 1

[h.mon]

You are missing an output file name after --domtblout:

hmmscan --cpu 16 \
  --domtblout pfam.domtblout \
  /scratch/slin023/trinotate/Pfam-A.hmm \
  /scratch/slin023/PhormiaCodingRegion/Phormia_de_novo_transcriptome_assembly_V1.fasta.transdecoder.pep \
  > pfam.log

[slin023]

That fixes the error and the hmmer is processing now. Thank you so much for your help!