rnammer error :the command line on the script does not work

Question

[slin023]

Hi,

I am new to bioinformatics

I used a SLURM script from a website to identify ribosomal RNA by rnammer

However, it doesn't work very well, clearly the command line is wrong based on log file

/home/share/slurm/19.05.3/share/man /tmp/slurmd/job1653084/slurm_script: line 12: /scratch/slin023/trinotate//RnammerTranscriptome.pl: Permission denied

I tried to compare with other rnammer website, but I am very confused with the command line, any help or guide is welcome, I will sincerely appreciate it, here are the script:

#!/bin/bash
##SBATCH --qos pq_mdegenna
##SBATCH --account iacc_mdegenna
#SBATCH -n 1
#SBATCH -N 1
#SBATCH --mem 5000

## Run RNAMMER 1.2 to identify rRNA transcripts
module load rnammer/1.2

/scratch/slin023/trinotate/RnammerTranscriptome.pl \
    --transcriptome /path/to/Phormia_de_novo_transcriptome_assembly_V1.fasta \
    --org_type euk \
    --path_to_rnammer /home/share/Modules/3.2.10/modulefiles/rnammer/1.2

Here are the things I would like to address first:

• I didn't find RnammerTranscriptome.pl on SLURM Trinotate file, so I downloaded RnammerTranscriptome.pl from Trinotate and moved it to my folder
• I am not sure if path_to_rnammer on the script is correct, but the command I provided is the directory I found on SLURM

[karl.stamm]

The error says permission denied. That's your operating system saying No to running that command. The file is not executable, or the folder is restricted. I'm tempted to say this isn't a bio-informatics issue at all, but a simple sysadmin issue. Not Mummer's fault your system setup is incomplete. But to try to be helpful, look up "chmod +x" for your .pl file. It probably has more problems, but we can fix the permission denied error with a chmod.

[slin023]

Hi, Karl, thanks for the feedback, I tried to use "chmod +x" on my .pl file, but it still doesn't work. This is the log message:/home/share/slurm/19.05.3/share/man /tmp/slurmd/job1653144/slurm_script: /scratch/slin023/trinotate/RnammerTranscriptome.pl: /opt/conda/conda-bld/trinotate_1596012853563/_h_env_placehold_placehold_placeh: bad interpreter: No such file or directory

[karl.stamm]

As I said, it probably has more problems within the script, now you've got "bad interpreter: No such file or directory" and we've fixed the original error of permission Denied. Moving the file "from Trinotate" gave you a funny/broken edition.

[slin023]

so you mean the .pl should not be moved out from the Trinotate file? and I have to locate the Trinotate in SLURM and find out the directory of RnammerTranscriptome.pl