[ensembl-dev] [External] Re: 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.

Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF) ctatters at bidmc.harvard.edu
Wed Jun 30 18:30:11 BST 2021


Hi Diana,

Thank you for your reply. Here is my PERL5LIB

```
/home/ct194/perl5/lib/perl5:/home/ct194/perl5/lib/perl5:/home/ct194/src/bioperl-1.6.924:/home/ct194/src/ensembl/modules:/home/ct194/src/ensembl-compara/modules:/home/ct194/src/ensembl-variation/modules:/home/ct194/src/ensembl-funcgen/modules:/home/ct194/src/ensembl-taxonomy/modules:/home/ct194/src/ensembl-metadata/modules:/home/ct194/src/ensembl-io/modules:/home/ct194/src/Bio-DB-HTS/lib:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx
```
I seem to be getting a new exception now.
Exception:
'Can't locate Try/Tiny.pm in @INC'

Best,
Calum


________________________________
From: Diana Lemos <dlemos at ebi.ac.uk>
Sent: Wednesday, June 30, 2021 12:12 PM
To: Ensembl developers list; Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF)
Subject: [External] Re: [ensembl-dev] 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.


Hello Calum,


Can you please share what you have in your PERL5LIB? (echo $PERL5LIB)



Kind Regards,

Diana




On 30/06/2021 16:19, Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF) wrote:

Bash on Linux version 7 with Perl/5.24.0. Attempting to access 1000 Genomes population frequencies using example script from


https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/<https://urldefense.com/v3/__https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7MoRoy30$>


The API version used is 104.


Error message is

'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor'  cannot be found.


Exception is

'Can't locate Bio/DB/HTS/Tabix.pm in @INC'


BEGIN failed--compilation aborted at /src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 41.

BEGIN failed--compilation aborted at /src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 42.

Compilation failed in require at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 82.
BEGIN failed--compilation aborted at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 82.
Compilation failed in require at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 98.
BEGIN failed--compilation aborted at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 98.
Compilation failed in require at (eval 875) line 2.


I have been unable to clone tabix from github, but their page says it has been moved to htslib. I made htslib following api installation instructions here:

https://useast.ensembl.org/info/docs/api/api_installation.html<https://urldefense.com/v3/__https://useast.ensembl.org/info/docs/api/api_installation.html__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7DS6ergQ$>


Thanks,

Calum

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