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197

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How to run beast.jar file using Slurm?

phylogeny hpc slurm beast jar written 6 weeks ago by kabir.deb0353 • 0

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111

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How to run 2 programme one after another using single SLURM?

slurm parallel written 25 days ago by kabir.deb0353 • 0 • updated 24 days ago by Mensur Dlakic • 2.9k

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108

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How much memory / how many cores should I request for peak calling?

slurm chip-seq written 7 weeks ago by jrleary • 40 • updated 7 weeks ago by genomax ♦ 76k

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419

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6 follow

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Python and SLURM environment : clarifications needed

python slurm written 4 months ago by Rox • 1.1k • updated 3 months ago by Biostar ♦♦ 20

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306

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toil-cwl-runner on slurm: toil.batchSystems.singleMachine maxMemory limit?

toil slurm cwl singularity written 6 months ago by alanh • 80 • updated 6 months ago by Michael R. Crusoe • 1.8k

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1.6k

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CWL: SLurm Job Sheduler

slurm cwl written 2.6 years ago by kevin.o.oluoch • 70 • updated 8 months ago by Biostar ♦♦ 20

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440

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How to call a R variable in a loop with Slurm?

R slurm matrix written 8 months ago by vincentpailler • 110

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436

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7 follow

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Distribute proportionality calculations on many nodes (SLURM)

matrix slurm correlation parallelization written 9 months ago by vincentpailler • 110 • updated 9 months ago by Jean-Karim Heriche ♦ 21k

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288

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slurm Exceeded step memory limit: Interleaving FastQ files

fastq slurm written 9 months ago by Biogeek • 380

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974

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snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Error submitting jobscript (exit code 1):)

software error slurm snakemake written 10 months ago by Berghopper • 20

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360

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Best way running OMA using SLURM

oma slurm written 11 months ago by dimar.gonzalez.soto • 0 • updated 11 months ago by adrian.altenhoff • 620

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1.8k

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6 follow

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How to submit multithreaded jobs on SLURM and determine number of threads?

slurm written 16 months ago by steve • 2.4k • updated 16 months ago by Devon Ryan ♦ 93k

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945

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usage of OMA on a HPC cluster with slurm

oma slurm written 2.1 years ago by Yang • 0

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971

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Failure to launch OMA in array mode on SLURM cluster

orthologs oma slurm written 2.2 years ago by jeremias.br • 10

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1.0k

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Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment

slurm parallelization meme parallel tutorial written 2.3 years ago by Alex Reynolds ♦ 29k

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4.5k

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How to set $TMPDIR in a parallel processing

hpc gun parallel slurm written 4.5 years ago by lisadavic66 • 0 • updated 2.8 years ago by el.unico.joe • 0

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608

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any recommendations about public computer clusters?

slurm computer cluster written 2.8 years ago by vmicrobio • 240

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1.5k

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Cufflinks: exceeded memory limit (31836604 > 31457280), being killed

memory limit cufflinks slurm written 3.7 years ago by debitboro • 160

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1.6k

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Errors attempting to start OMA job on SLURM-managed cluster

oma slurm written 3.9 years ago by Adamc • 640 • updated 3.8 years ago by adrian.altenhoff • 620

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Recent Replies

C: Is it possible to download nr db from NCBI's cloud ? by K.Gee • 10
Thanks for the response. My problem is that im not so familiar with informatics, so I was thinkin...
C: DE genes and variability between biological replicates: edgeR by mariannapauletto • 20
Thank you, sorry for that
A: Ambiguous fields in FANTOM 5 Enhancer_TSS_association.bed file by Corentin • 430
Hi, The file is in the BED12 format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 . This fo...
C: Is it possible to remove reads from BAM which match the reference at a position by yryan • 0
That worked perfectly, thanks so much for that!
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
It is certainly possible that you have bad/less than optimal data. If you get a similar result wi...
C: Google Summer of Code 2020 announced for mentor organisations by Emily_Ensembl ♦ 20k
Mentor applications are now open and will be open until 5th February.
C: Possible reasons mapping percentage abysmally low for miRNA reads? by Cookie-san • 40
So you think the problem is with the aligner and not the data? I will try bbmap.sh as you suggest...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
If you are willing to try a different aligner then you could try using `bbmap.sh` with these para...
C: Case control status permutation in GWAS by German.M.Demidov • 1.2k
Aren't you supposed to calculate p-values from the permuted data? And then just use Manhattan plot?
C: GATK HaplotypeCaller/GenotypeGVCFs assigning GQ 0 and GT ./. at well-covered, hi by Dataman • 310
I have also recently encountered this problem. Did you find out the answer to your question? It s...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by Cookie-san • 40
mapper.pl from miRDeep2 uses bowtie (1). Seed length is 18bp, and it allows no mismatch in this a...
C: Possible reasons mapping percentage abysmally low for miRNA reads? by genomax ♦ 76k
What aligner are you using? Is it doing ungapped alignments as would be needed for reads ~18 bp?

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