Closed JaMaack closed 2 years ago
Hi @JaMaack ! Thanks for using the pipeline, we just recently added VarSkipV2
so need to look into this.
@oliverdrechsel @MarieLataretu maybe there is still something misformatted with the BED file that does not work well with the ARTIC pipeline? Can you please compare it with the BED file that you were finally able to run?
@JaMaack can you please provide the error log? E.g. via
cat work/71/0aad14*/.command.log
that should give you information on one of the failed processes.
Hi all
I'll send the bed file we used for our runs that worked well. Would be nice, if we could swap it with the current one as I'm sure it works fine then.
Cheers.
Martin Hölzer @.***> schrieb am So., 30. Jan. 2022, 18:32:
Hi @JaMaack https://github.com/JaMaack ! Thanks for using the pipeline, we just recently added VarSkipV2 so need to look into this.
@oliverdrechsel https://github.com/oliverdrechsel @MarieLataretu https://github.com/MarieLataretu maybe there is still something misformatted with the BED file that does not work well with the ARTIC pipeline? Can you please compare it with the BED file that you were finally able to run?
@JaMaack https://github.com/JaMaack can you please provide the error log? E.g. via
cat work/71/0aad14*/.command.log
that should give you information on one of the failed processes.
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@JaMaack could you try running poreCov via -r customBED --primerV VarSkipV2
Hi, I've been trying to run the pipeline with
--primerV VarSkipV2
. However, the run always prematurely stops at the variant calling step. The respective line reads[71/0aad14] process > artic_ncov_wf:artic_medaka (23) [100%] 23 of 23, failed: 23 ✔
. It worked perfectly fine with the VarSkipV1 option and I haven't changed anything else. I'm not really sure what the issue is, here.