Files not found about gapseq HOT 6 CLOSED

The files are usually downloaded when they do not exist. Can't reproduce the error, what exactly did you do?

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I just run the command /home/***/software/gapseq/gapseq doall /home/***/software/gapseq/toy/myb71.fna.gz
testgapseq.err.txt

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what is the output if you run ./src/update_sequences.sh manually and does the error reproduce afterwards?

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Hi,
I ran the above command and fixed the errors as shown in the error file. Now it returns:

slurmstepd: error: _is_a_lwp: open() /proc/21577/status failed: No such file or directory
slurmstepd: error: _is_a_lwp: open() /proc/19803/status failed: No such file or directory
index file myb71.fna.tmp.fai not found, generating...
I think it seems ok, isn't?

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Hi,
i also get this slurmstepd error. I'm looking into it...

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okay,
I found this:

Possible causes/remedies:

_is_a_lwp is a function called internally for Slurm job accounting. The message indicates a rare error situation with a function call. But the error shouldn't affect anything in the user job. Please ignore the message.
(https://docs.nersc.gov/jobs/jobs-faq/)

Even though, this issue isn't technically closed, I will close it here since it seems that it does not directly stem from gapseq and since it seems not to affect gapseq outcomes.

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