Comments (8)
Yes, @wikiselev shared his rnaseq implementation with me.
from methylseq.
Hi Phil,
Thanks for the quickfix, I have already tried the commit from your master branch and it worked fine.
We have now fully working methylseq pipeline implemented in openstack using WR in our group.
Thanks for your continuous support.
Cheers,
Shriram
from methylseq.
Fantastic! Thanks for letting us know.. And great that you guys are able to use this in production! 😄
I hadn't realised that you were also at the Sanger until now. Are you already in contact with @wikiselev and @micans? They're also running nf-core pipelines on your OpenStack / Kubernetes infrastructure..
from methylseq.
Hi @sb43,
Thanks for reporting this. I guess that it's not that samtools is being inefficient, but more that we're telling samtools to use exactly the amount of memory available, to the byte:
Lines 774 to 777 in 1d3f5cc
In most computational setups, the memory allocation is a little relaxed meaning that this isn't a problem, but we have seen similar problems in other pipelines. I guess that just reducing the requested amount a little should fix the problem. In fact, @apeltzer did exactly this in the rnaseq pipeline the other day: nf-core/rnaseq#158
Phil
from methylseq.
Hi @ewels,
Shall I create custom main.nf as suggested nf-core/rnaseq#158 , currently I am using methylseq v1.3 --with-docker using default main.nf.
OR
Have you planned a bugfix release anytime soon?
Thanks,
Shriram
from methylseq.
Ok, pull-request merged. You should now be able to run this now using nextflow run nf-core/methylseq -r dev
(the -r dev
will pull the development version of the code). It will then go out in the next stable release, which should be relatively soon I think.
I'll close this issue now, but let me know if you hit any problems and we can reopen. Would be great to hear how you get on too!
Cheers,
Phil
from methylseq.
from methylseq.
It seems this issue has returned. I am running into the same situation where samtools sort requests exactly as much memory as was reserved for the task (or a little more), resulting in the task being killed. If I'm interpreting things correctly, the changes added in PR #82 got lost when the NextFlow configuration was split into modules. See here: https://github.com/nf-core/methylseq/blob/81f989c93e866a9b0bd0d9584e077b9b8f78affe/modules/nf-core/samtools/sort/main.nf#L24C33-L24C33
from methylseq.
Related Issues (20)
- Support for NuGEN Ovation RRBS HOT 2
- samplesheet input is not detecting entire values in sample column HOT 6
- Create metro map HOT 1
- Add gemBS option
- CG CHG and CHH with --comprehensive flag using bismark workflow HOT 8
- --rrbs and --emseq parameter and argument usage
- typo in samplesheet in README.md?
- Latest template merge completely broke dev branch (on AWS + Fusion) HOT 4
- Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency HOT 1
- Schematic for the methylseq pipeline
- bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. HOT 2
- AS-XS tag missing
- Write tests for samplesheet sample merging/grouping
- Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option)
- Bwameth vs bismark HOT 1
- Multiple issues in the pipeline HOT 1
- samplesheet handling: different path + same filename gives an error
- Pipeline requires 72GB of RAM, even to test. HOT 1
- Preseq error
- Massive disk usage
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from methylseq.