Error in 3-alignTips phase
Closed this issue · 5 comments
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?
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.
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
What was your linux version/type? I think Ubuntu is usually the one where sh links to dash not bash.
It is Ubuntu 20.04.5 LTS