Felix Krueger

Whoah, that looks quite wild indeed. Judging by the sequence composition, it doesn't look like a standard sequencing protocol, it rather looks like amplicon sequencing to me. Any chance this...

Good morning both. I don't think we have actively used the NEB EM-kit nor the Diagenode RRBS kit outselves, but I seem to recall that a few issues with these...

here is one, cheers. [cf_bismark_singlecell_1488545447_submissionlog.txt](https://github.com/ewels/clusterflow/files/816812/cf_bismark_singlecell_1488545447_submissionlog.txt)

Are you sure you want this? ^^ [CF_qstat.txt](https://github.com/ewels/clusterflow/files/816938/CF_qstat.txt) [qstat.txt](https://github.com/ewels/clusterflow/files/816939/qstat.txt)

I see this: ``` Cluster Flow ID: bismark_singlecell_1488545447 Submitted Jobs: 902 Running Jobs: 77 Queued Jobs: 1095 (resources) Completed Jobs: -270 (-29%) ====================================================================== - bismark_align [4 cores] [queued, priority 0]...

yes sorry, it's not like I have nothing to do... :)

Here you go: [qstat.txt](https://github.com/ewels/clusterflow/files/816980/qstat.txt)

Hmm, this is a tricky question. Frankly, I don't think SNPsplit is suited for this kind of scenario (long, noisy reads) and there is little if any functionality currently to...

Hmm this is tricky to debug, but my guess would be that you are running out of memory. On what kind of system are you running this on? I would...

Just for your information, there is still an open issue (https://github.com/FelixKrueger/Bismark/issues/638) describing a memory leak specifically with Bowtie 2 v2.5.2. Is there a chance you ran into the same issue?