Variant calling doesn't seem to work with VarSkipV2

[JaMaack]

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.

[hoelzer]

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.

[oliverdrechsel]

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. — Reply to this email directly, view it on GitHub <#210 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB57EEIGJ7YFEVYDCFHIX6DUYVY4HANCNFSM5NEIBL3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[replikation]

@JaMaack could you try running poreCov via -r customBED --primerV VarSkipV2

• the primer did work on my end
• we merge this after some testing into a release