Skip to content
This repository was archived by the owner on Jan 27, 2020. It is now read-only.

Changing VEP to v92 and adjusting CPUs #678

Merged
szilvajuhos merged 13 commits intoSciLifeLab:devfrom
szilvajuhos:master
Nov 2, 2018
Merged

Changing VEP to v92 and adjusting CPUs #678
szilvajuhos merged 13 commits intoSciLifeLab:devfrom
szilvajuhos:master

Conversation

@szilvajuhos
Copy link
Copy Markdown
Collaborator

@szilvajuhos szilvajuhos commented Oct 31, 2018 •
edited
Loading

PR checklist

  • PR is made against dev branch
  • Looks Singularity v2.5 and VEP 91 are not able to work together, so both needed version update
  • Ensure the test suite passes (./scripts/test.sh -p docker -t ALL).
  • Documentation in docs is updated
  • CHANGELOG.md is updated

@szilvajuhos
Copy link
Copy Markdown
Collaborator Author

szilvajuhos commented Oct 31, 2018

I had continuous serialization errors with Singularity 2.5.1 and VEP 91 like:

-------------------- EXCEPTION --------------------
MSG: ERROR: Inappropriate ioctl for device
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::deserialize_from_file_storable /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:134
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::deserialize_from_file /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:103
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::get_features_by_regions_uncached /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:261
STACK Bio::EnsEMBL::VEP::AnnotationSource::get_all_features_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm:134
STACK Bio::EnsEMBL::VEP::AnnotationType::Transcript::annotate_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm:101
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:402
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:364
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel /opt/vep/src/ensembl-vep/vep:224
Date (localtime)    = Fri Oct 26 16:49:30 2018
Ensembl API version = 93

The solution is apparently to

  • change to Singularity 2.6
  • change to VEP 92

VEP is actually at 94.4, but changing I do not dare to change to it right now. Note, we are running forked version of VEP now, that speeds up processing, but for some reason it is still slow. @maxulysse you have to change the current default vepgrch38 container also.

@szilvajuhos szilvajuhos requested a review from maxulysse October 31, 2018 09:56
@szilvajuhos szilvajuhos merged commit 436cf23 into SciLifeLab:dev Nov 2, 2018
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.

Reviewers

1 more reviewer

@maxulysse maxulysse maxulysse approved these changes

Reviewers whose approvals may not affect merge requirements

Assignees

No one assigned

Labels

ready to merge

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@szilvajuhos @maxulysse
⚡