Batch job submission failed: Invalid account or account/partition combination specified

[Евгения Головина]

Hi there,

I'm trying to run juicer on our University cluster using your test files but get a sbatch error on the dedup step (alignments and everything before dedup step looks like going right). Can you please look into my juicer.sh script and help me to figure out this problem. I have no idea what I'm doing wrong. Script and dedup.err/out files are attached. Thank you!

juicer.sh script is here.
dedup-###.err looks like this.
dedup-###.out looks like this.


Best wishes,
Evgeniia

[Neva Durand]

I have never seen this error before.  It's possible your system is set up such that you cannot launch a job from another job (which is what happens in the dedup script).  I suggest talking to your IT people to see what this could be.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Евгения Головина]

Hi,

Actually, I found out the reason. 

Taking a closer look at the longest line of that script I see it calls the awk script juicer/SLURM/scripts/split_rmdups.awk. It didn't occur to me to look there before, but that script includes calls to sbatch, so I guess that is where the error is arising.

So I just needed to get the my account details setting into these somehow. A simpler fix was to add 

export SBATCH_ACCOUNT=#### into the DEDUP batch file before the call to awk. That setting will then be inherited by the awk process and its child sbatch processes.

пятница, 16 февраля 2018 г., 11:17:14 UTC+13 пользователь Евгения Головина написал:

[Neva Durand]

Glad to hear it!  Thanks for posting back again.

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