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Use of uninitialized value $preseq in substr at ...TranscriptVariationAllele.pm line 2187 #1457
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Same here. Is it possible to fix this "spam"? Or what is the reason for such messages? |
Thanks @Stikus @serge2016 for reporting this issue! This is a warning and does not effect output. It is generated during calculation of HGVS notation when there is no extraneous matching sequence between ref and alt alleles - which is actually the common case. It is quite a misleading message. We will put a fix in place and let you know. Best regards, |
@nakib103 Thanks for fast answer, we'll wait for fix. Btw - someone forgot to mark 110 release as latest: And I cannot reopen #1350 (comment) this issue, but we still have problem with |
Thanks @Stikus, the tag has been placed. Best regards, |
Hello @Stikus @serge2016 , A new version of VEP 110.1 is available with the fix. Please upgrade your VEP installation to this version and let us know if that fixes your issue. If you are using docker image you can just pull the latest image and it will contain the fix.
If you have installed VEP from the command line make sure you also update the API when updating VEP to latest version.
Best regards, |
All good now, thx:
|
Describe the issue
After 110 VEP release we start catching a lot of warnings we haven't catch before:
Additional information
Looks like the reason is behind these new lines in TranscriptVariationAllele.pm:
diff link
$preseq
somehow left uninitialized.System
Full VEP command line
Full error message
Data files
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