[ensembl-dev] error in Ensembl 96 - missing ref or alt allele in vcf

Honysová, Barbora Barbora.Honysova at gennet.cz
Tue May 7 14:42:56 BST 2019 

Dear developers,

I have installed new version of VEP. I have tried to check the installation by my control.vcf which worked quiet well till Ens95. I have not changed anything in config file (just the version), but I am not able to receive results for all the variants in vcf.
I am sending the control.vcf as attachment as well, where I have checked ref and alt alleles.

There is the output:


bhonysova at srvlnx01:/data/src/ensembl-vep-96$ ./vep -i control.vcf -o control_config_new_dbnsfp.txt --config config_new_dbnsfp.txt --verbose
Will only load v96 databases
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_96_38'
Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_96_38'
Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_96_38'
Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_96_38'
homo_sapiens_variation_96_38 loaded
homo_sapiens_funcgen_96_38 loaded
No ancestral database found
No ontology database found
No taxonomy database found
No ensembl_metadata database found
No production database or adaptor found
2019-05-07 15:33:31 - Auto-detected FASTA file in cache directory
WARNING: No input file format specified - detected vcf format
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-------------------- EXCEPTION --------------------
MSG: Missing reference or alternate sequence
STACK Bio::EnsEMBL::Variation::Utils::Sequence::trim_sequences /data/src/ensembl-vep-96/Bio/EnsEMBL/Variation/Utils/Sequence.pm:943
STACK Bio::EnsEMBL::Variation::Utils::Sequence::get_matched_variant_alleles /data/src/ensembl-vep-96/Bio/EnsEMBL/Variation/Utils/Sequence.pm:1125
STACK Bio::EnsEMBL::VEP::AnnotationType::Variation::compare_existing /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/AnnotationType/Variation.pm:176
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::VariationTabix::_annotate_pm /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/VariationTabix.pm:239
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::VariationTabix::annotate_InputBuffer /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/VariationTabix.pm:120
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:402
STACK (eval) /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:663
STACK Bio::EnsEMBL::VEP::Runner::_forked_process /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:657
STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:488
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:361
STACK Bio::EnsEMBL::VEP::Runner::run /data/src/ensembl-vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel ./vep:218
Date (localtime)    = Tue May  7 15:34:06 2019
Ensembl API version = 96
---------------------------------------------------
Died in forked process 44402

Please, could you help me to find the error causing the interuption of annotation process?
Thank you in advance.

Bara




Ing. Barbora Honysová

Odborný VŠ pracovník - bioinformatik

GENNET, s.r.o.



Kostelní 9, 170 00 Praha 7
Tel: +420 222 313 000

www.gennet.cz<http://www.gennet.cz>



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