Job Commands Not Found

[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?

[brianjohnhaas]

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

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On Mon, Apr 29, 2019 at 10:48 AM nadeaue ***@***.***> 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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#19>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKXZJG7HCA2EX5NTN3Y3PS4DE3ANCNFSM4HJD74CA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[nadeaue]

Hi Brian,

You were right about the ''. I had an additional space after some of them and didn't notice, but I fixed it and it's running now.

Thanks,
Emily

[brianjohnhaas]

great! best of luck

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On Mon, Apr 29, 2019 at 10:58 AM nadeaue ***@***.***> wrote: Hi Brian, You were right about the ''. I had an additional space after some of them and didn't notice, but I fixed it and it's running now. Thanks, Emily — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#19 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKX6IVZG7AQJ7LSJ3CYDPS4EKTANCNFSM4HJD74CA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>