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.