Comments (4)
willmclaren
commented on August 14, 2024
Strange, does the same happen if you start again from scratch?
Travis doesn't report this and neither do my tests. I can put in some code that should mean this won't die like this but it would be good if we could understand why!
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henrikstranneheim
commented on August 14, 2024
Yes, it does. I removed the entire dir and cloned it again but the error persists.
/H
Skickat från min iPhone
… 12 dec. 2016 kl. 14:16 skrev William McLaren ***@***.***>:
Strange, does the same happen if you start again from scratch?
Travis doesn't report this and neither do my tests. I can put in some code that should mean this won't die like this but it would be good if we could understand why!
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henrikstranneheim
commented on August 14, 2024
This might be related: Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at perl-5.18.2/lib/5.18.2/x86_64-linux/DynaLoader.pm line 213.
/H
On 12 Dec 2016, at 14:16, William McLaren ***@***.***> wrote:
Strange, does the same happen if you start again from scratch?
Travis doesn't report this and neither do my tests. I can put in some code that should mean this won't die like this but it would be good if we could understand why!
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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAjsImbm5JI6aMhePWm8EWy8AhZXWa_Kks5rHUkxgaJpZM4LKXxi>.
Henrik Stranneheim Ph.D. Senior Bioinformatician
Department of Molecular Medicine and Surgery
Karolinska Institute
Science for Life Laboratory
E-mail: [email protected] <mailto:[email protected]>
Visiting address:
Science for Life Laboratory - SciLifeLab
Gamma building
Tomtebodavägen 23A
Delivery address:
Science for Life Laboratory - SciLifeLab
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willmclaren
commented on August 14, 2024
OK thanks.
This should be fixed by d80fde0
I haven't seen that warning before, but that type usually is nothing to worry about. Unfortunately it is coming from the bioperl module over which we have no control, so it is more difficult to get a fix for.
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Related Issues (20)
- Custom VCF w/overlap joins multiple FILTER values for a record with same delimiter ("&") as other records HOT 2
- Normalization of VCF file HOT 2
- VEP VCF output
- dbNSFP plugin not getting results for specified columns HOT 14
- Need to add sample specific genotype information to the data frame generated using VEP annotated vcf file. HOT 14
- Using one of the two annotation sources VCF is used when same annotation source name is used HOT 5
- output HGVSp nomenclature is non-standard HOT 2
- VEP version 111 outputs HGVSg substitution instead of deletion for one out of the two alternative allele deletions HOT 6
- VEP version 111 outputs HGVSp duplications not following the 3' rule in regions of repeated aminoacids HOT 2
- Haplo results interpratation HOT 1
- Use of uninitialized value at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/IO/Parser/GTF.pm HOT 4
- Can't locate Bio/EnsEMBL/Utils/Exception.pm in @INC HOT 2
- Homo Sapiens GRCH38 Merged Cache Installation Failing on CHECKSUMS HOT 10
- Outdated or missing genes when using RefSeq cache HOT 5
- You must specify a region in the format chr, chr:start or chr:start-end at perl5/5.32/site_perl/Bio/DB/HTS/Tabix.pm line 104 HOT 3
- Different output results between only used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz and used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz with other database HOT 5
- WARNING: Chromosome ? not found in annotation sources or synonyms on line ? HOT 2
- the web file has no image HOT 5
- Alternative allele of matched variants is not reported in custom annotation with overlap method HOT 1
- Nextflow Failing with Missing Output File HOT 9
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