brianjohnhaas
commented
5 years ago Hi,
It looks like the slurm submission script might be misformed as it thinks the parameters are different commands. If you're using '\' to escape the newline and put parameters on different lines, be sure the '\' is directly before the newline. Alternatively, don't escape newlines and put all the parameters on the same line.
If the above isn't relevant to your situation, just share your submission script with me and I'll hopefully see what the problem is.
bhaas@broadinstitute.org
best,
~b
On Mon, Apr 29, 2019 at 10:48 AM nadeaue notifications@github.com wrote:
I'm attempting to run the blastx search. I ran blastp with no problem, but I've now received the following errors in my slurm file:
Error: Too many positional arguments (1), the offending value: Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /var/spool/slurm/d/job102720/slurm_script: line 22: -db: command not found /var/spool/slurm/d/job102720/slurm_script: line 23: -num_threads: command not found /var/spool/slurm/d/job102720/slurm_script: line 24: -max_target_seqs: command not found /var/spool/slurm/d/job102720/slurm_script: line 26: -evalue: command not found
My blastp script contains these commands and completed, and they're the same ones listed on the help page to complete both searches. Should I try different commands?
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nadeaue
I'm attempting to run the blastx search. I ran blastp with no problem, but I've now received the following errors in my slurm file:
Error: Too many positional arguments (1), the offending value:
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value:
/var/spool/slurm/d/job102720/slurm_script: line 22: -db: command not found /var/spool/slurm/d/job102720/slurm_script: line 23: -num_threads: command not found /var/spool/slurm/d/job102720/slurm_script: line 24: -max_target_seqs: command not found /var/spool/slurm/d/job102720/slurm_script: line 26: -evalue: command not found
My blastp script contains these commands and completed, and they're the same ones listed on the help page to complete both searches. Should I try different commands?