Dmitry Antipov

actually k=71 worked only in the sense that it did not crash. Results are irrelevant unique 0 (exactly one instance of the kmer is in the input) distinct 1458 (non-redundant...

Can add onerror in snakemake files for better time/memory limit

This issue is not related. One of your runs crashed with unknown reason, right? Let's create a separate issue for it. Missing runRDNAMashMap is optional and is not run without...

we already have --latency-wait 30 snakemake as default option for cluster runs, so adding --snakeopts "-latency-wait 3" should not help.

Could you show 8-hicPipeline/splitHIC.err and 8-hicPipeline/splitHIC.sh ? Not sure that I get the question about submitting jobs directly. Snakemake submits splitHIC.sh script, which is generated at the splitHIC checkpoint (and...

> [splitHIC.zip](https://github.com/marbl/verkko/files/14795734/splitHIC.zip) I was more interested in files from 8-hicPipeline/ folder; 8-hicPipeline/splitHIC.err is not copied to batch-scripts If it survived the rerun, we can try to find out what was...

So, empty .err file and it looks like the splitHiC process did not even start here... Does this problem happen with all the verkko HiC runs on your system, or...

if there is a problem with sh my question is why it didn't crash before.. Is it possible that sh interpreter is not available as /bin/sh on some subset(but not...

Hi, Since this tool was released in 2021 and didn't receive significant updates, I'd also recommend for checking newer alternatives. If you are still interested to run exactly viralVerify, I'd...

I'm pretty sure that plasmidVerify would also classify it as plasmid. For the sequences that similar to both P and V and not similar to C a plasmid prediction tool...