marbl/verkko

Error in 3-alignTips phase

Closed this issue · 5 comments

jlipovac commented

Hi,

I was running verkko 1.4.1 version and using duplex reads (>=10kb) as --hifi input (also providing UL reads >= 50kbp as --nano input).
I got the same error mentioned in the issue #185.

Here is the snakemake log output:
2023-08-19T135407.106912.snakemake.log

I reran it with verkko 1.4.0 and it is running normally.
Any idea what could be an issue?

skoren commented

What's the contents in 3-alignTips folder and the output in 3-alignTips/splitONT.err? I think it's the same sh not being bash on the system. The set pipefail options are new to 1.4.1 and aren't in 1.4.0. As long as the jobs completed and there are no error messages in any of the *.err files in the 3-alignTips folder, 1.4.0 results should be OK to use.

jlipovac commented

I've already rerun verkko with 1.4.0 version and with the same output dir so I don't have the content of 3-alignTips folder from that moment. If I run verkko again soon I'll try with sh/bash replacing

skoren commented

What was your linux version/type? I think Ubuntu is usually the one where sh links to dash not bash.

jlipovac commented

It is Ubuntu 20.04.5 LTS

skoren commented

Yeah, I'm pretty sure then it's the same as #185 and is due to using sh not bash. I'll close this one and track it together with #185.

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