HMMER software error message

Question

[a.mostafa5050]

Hi everybody, I am running the HMMER to search for protein sequence against resfam database.

I got the following error message

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

I would be grateful if anyone can help me solve this.

This is my script

#!/bin/sh
#SBATCH --job-name=HMMER_ahmed
#SBATCH --account=nn9787k
#SBATCH --time=08:30:00
#SBATCH --mem-per-cpu=4G
#SBATCH --output=slurm-%j.base

## Set up job environment:
module load HMMER/3.2.1-foss-2018b
##Running HMMER
hmmpress /cluster/work/users/ahmedbar/Resfams-full.hmm
hmmscan --cut_ga --tblout s–o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R \
/cluster/work/users/ahmedbar/Resfams-full.hmm \
/cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_fasta/prokka_F-1year_Amox.fasta \

[Ram]

Your command is incomplete - the hmmscan command ends in a back-slash that tells the shell that you're not done typing the command (like a "to be continued"). Remove that and see if that helps.

Also, please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[a.mostafa5050]

I removed the back-slash and still gives me the same error message!

this is the new script

#!/bin/sh
#SBATCH --job-name=HMMER_ahmed
#SBATCH --account=nn9787k
#SBATCH --time=08:30:00
#SBATCH --mem-per-cpu=4G
#SBATCH --output=slurm-%j.base

## Set up job environment:
module load HMMER/3.2.1-foss-2018b
##Running HMMER
hmmpress /cluster/work/users/ahmedbar/Resfams-full.hmm
hmmscan --cut_ga --tblout –o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R /cluster/work/users/ahmedbar/Resfams-full.hmm /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_fasta/prokka_F-1year_Amox.fasta

[Mensur Dlakic]

You need a file name after --tblout and before -o.

Answer 1

[Mensur Dlakic]

Like @_r_am said, please invest some time into formatting your questions so it is clear what you are asking. I did a quick look at your initial post and decided it was too much work to decipher what was wrong. Now that it is formatted, it is easier to see where the likely error is.

--tblout s–o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R

This part of your command is telling the program to save the table-formatted output into file s–o, and since there is no switch after that it is interpreting the next portion as your database. Chances are that s–o needs to be s –o in which case /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R is likely the file where you want the regular output saved. The short of it is that you most likely need an extra space before -o. If that still doesn't solve the problem, I think you should verbalize exactly what you are trying to do with this command as it is difficult to help otherwise.

By the way, it might be nice to acknowledge what @_r_am did for your original post.

Answer 2

[Fatima]

-o is redundant as you are using --tblout

This should work:

  hmmscan --cut_ga --tblout /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R /cluster/work/users/ahmedbar/Resfams-full.hmm /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_fasta/prokka_F-1year_Amox.fasta

Also since you're using --cut_ga, you need to make sure Resfams-full.hmm contains "GA" values.

[a.mostafa5050]

sorry for the bad formatting in the previous two posts. I really appreciate your quick response. I tried the command you gave me, but still, the same error message appears. I would like to annotate protein sequences using the Resfams database.

[Fatima]

Can you try without --cut_ga and see if it works?

Also please make sure HMMER_R is not a folder. For --tblout you need to specify a file name, so if HMMER_R is a folder that path won't work.

[a.mostafa5050]

Yes, HMMER_R is a folder and I want the output files to be in it. so, which file should i add next to --tblout

[a.mostafa5050]

Thanks Fatima for helping. Really appreciate that. It worked, but I got another error message.

Failed to open tabular per-seq output file /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R for writing.

[Mensur Dlakic]

This was already explained: you can't save your output into a directory - it has to be a file. So if /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R is a directory, you need to add a file name at the end of it. Something like:

/cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R/file_name_output.txt

By the way, --tblout and -o are not redundant. You may wish to save table-formatted output in one file and regular output (alignments) in the other.

[Fatima]

Yes, but OP was using both for one file.