permissions errors loading jobs onto SLURM cluster at dedup stage

[Dane V]

Hi all, 

I am hoping someone can help us diagnose our issues running juicer v1.5.6 on our SLURM cluster without GPUs. 

We can successfully run juicer.sh up to the sorted merge point (our logs contain "Finished sorting all sorted files into a single merge" and the merged_sort.txt output looks complete) but we repeatedly encounter "sbatch: error: Batch job submission failed: Access/permission denied" errors in our logs at the deduping stage when juicer tries to split the merged_sort.txt and run deduping jobs on the cluster.

Looking at the sbatch scripts that are generated at this stage, everything seems to be OK and manually submitting these jobs to SLURM proceeds and appears to generate the correct output.

I am concerned about the sections of the split_rmdups.awk script that calls "#SBATCH -d singleton". I can only see one instance of "singleton" in juicer.sh (and this appears to be commented out on line 948 of juicer.sh v1.5.6). The following scripts created by the juicer.sh pipeline contain this call:

./.a1512542279_msplit.slurm

#SBATCH -d singleton

./.a1512542279_rmsplit.slurm

#SBATCH -d singleton

./.a1512542279_finalize.slurm

#SBATCH -d singleton

./.a1512542279_mail.slurm

#SBATCH -d singleton  

Its unclear to me if this might be part of the problem or a red herring. 

We are unclear how to proceed and any help would be appreciated.

Best wishes, 

Dane Vassiliadis. 

[Neva Durand]

Hello Dane,

I’m sorry you’re having problems. I’m not sure why singleton would cause a problem; we have not run into this. If you search on this page for “singleton”, you’ll see an explanation:

http://www.brightcomputing.com/blog/bid/174099/slurm-101-basic-slurm-usage-for-linux-clusters

Perhaps talk to the person that manages the clusters? The problem could be if jobs are not allowed to launch other jobs (though I would think this would have been a problem earlier in the pipeline).

You can run the dedupping without splitting. You would just run the dups script directly on the merged_sort file. This can take some time but might not be too terrible depending on how many reads you have and how many duplicates.

touch ${outputdir}/dups.txt
touch ${outputdir}/optdups.txt
touch ${outputdir}/merged_nodups.txt
awk -f ${juiceDir}/scripts/common/dups.awk -v name=${outputdir}/ ${outputdir}/merged_sort.txt
# for consistency with cluster naming in split_rmdups
mv ${outputdir}/optdups.txt ${outputdir}/opt_dups.txt

Then once the merged_nodups file is complete, relaunch Juicer in final mode by sending in the flag “-S final”

Best
Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org