[ensembl-dev] VEP error in TranscriptVariationAllele.pm

[Sarah Hunt]

Hi Michael,

Thanks for the detailed bug reports. These are now fixed in branch69 in CVS.

Best wishes,

Sarah

On Mon, Dec 31, 2012 at 1:10 AM, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> In Variant Effect Predictor 2.7 I get the following error, which appears to
> cause the program to stop when forking is on:
>
> ERROR: Forked process failed
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 923, <GEN1> line 5065.
>
> Without forking, the program doesn’t stop, but I still get the error, along
> with other related ones.
>
> The line that first complains is:
>   if($hgvs_notation->{type} eq "fs"){
> and $hgvs_notation->{type} does not exist.
>
> The offending VCF file is attached.
>
>
>
>
> TERMINAL OUTPUT (forking off):
> compute-4-46:myourshaw$ /home/myourshaw/apps/ActivePerl-5.16/bin/perl
> /share/apps/myourshaw/vax/vax.pl -input_file
> /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf
> -output_file
> /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf.vax
> --config /share/apps/myourshaw/vax/vep_lite.ini
> 2012-12-30 16:57:53 - Read configuration from
> /share/apps/myourshaw/vax/vep_lite.ini
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 2.7
>
> By Will McLaren (wm2 at ebi.ac.uk)
>
> Configuration options:
>
>
> canonical          1
> ccds               1
> check_alleles      1
> check_existing     1
> check_ref          1
> check_svs          1
> config             /share/apps/myourshaw/vax/vep_lite.ini
> core_type          core
> dir                /home/myourshaw/.vep
> domains            1
> force_overwrite    1
> format             vcf
> gene               1
> gmaf               1
> hgnc               1
> hgvs               1
> host               cortex.local
> input_file
> /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf
> no_progress        1
> numbers            1
> output_file
> /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf.vax
> password           ensembl
> plugin             vw
> Condel,/share/apps/myourshaw/VEP_plugins/config/Condel/config,b,2 VCFCols
> ExtraCols Consequences Conservation
> polyphen           b
> port               3306
> protein            1
> regulatory         1
> sift               b
> species            homo_sapiens
> terms              SO
> toplevel_dir       /home/myourshaw/.vep
> user               ensembl
> verbose            0
> xref_refseq        1
>
> --------------------
>
> 2012-12-30 16:57:53 - Connected to core version 69 database and variation
> version 69 database
> 2012-12-30 16:57:53 - Loaded plugin: vw
> 2012-12-30 16:57:53 - Loaded plugin: Condel
> 2012-12-30 16:57:53 - Loaded plugin: VCFCols
> 2012-12-30 16:57:53 - Fetching regulatory features for plugin: VCFCols
> 2012-12-30 16:57:53 - Loaded plugin: ExtraCols
> 2012-12-30 16:57:53 - Fetching regulatory features for plugin: ExtraCols
> 2012-12-30 16:57:53 - Loaded plugin: Consequences
> 2012-12-30 16:57:53 - Fetching regulatory features for plugin: Consequences
> 2012-12-30 16:57:53 - Loaded plugin: Conservation
> 2012-12-30 16:57:53 - Fetching regulatory features for plugin: Conservation
> 2012-12-30 16:57:53 - Starting...
> 2012-12-30 16:57:53 - Read 1 variants into buffer
> 2012-12-30 16:57:53 - Reading transcript data from cache and/or database
> 2012-12-30 16:57:53 - Retrieved 23 transcripts (0 mem, 0 cached, 23 DB, 0
> duplicates)
> 2012-12-30 16:57:53 - Reading regulatory data from cache and/or database
> 2012-12-30 16:57:53 - Retrieved 1 regulatory features (0 mem, 0 cached, 1
> DB, 0 duplicates)
> 2012-12-30 16:57:53 - Checking for existing variations
> 2012-12-30 16:57:53 - Checking for overlapping structural variations
> 2012-12-30 16:57:53 - Analyzing chromosome 3
> 2012-12-30 16:57:53 - Analyzing variants
> 2012-12-30 16:57:53 - Analyzing RegulatoryFeatures
> 2012-12-30 16:57:53 - Calculating consequences
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 923, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 927, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 945, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 959, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 963, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 756, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 772, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 809, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 828, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 923, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 927, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 945, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 959, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 963, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 756, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 772, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 809, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 828, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 923, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 927, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 945, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 959, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 963, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 756, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 772, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 778, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 809, <GEN1> line 60.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 828, <GEN1> line 60.
> 2012-12-30 16:57:54 - Processed 1 total variants (1 vars/sec, 1 vars/sec
> total)
> 2012-12-30 16:57:54 - Finished!
>
> ॐ
>
> Michael Yourshaw
>
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu
>
> 970.691.8299
>
> This message is intended only for the use of the addressee and may contain
> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY
> WORK PRODUCT. If you are not the intended recipient, you are hereby notified
> that any dissemination of this communication is strictly prohibited. If you
> have received this communication in error, please erase all copies of the
> message and its attachments and notify us immediately. Thank you.
>
>
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>