[ensembl-dev] VEP error in TranscriptVariationAllele.pm

Michael Yourshaw myourshaw at ucla.edu
Mon Dec 31 01:10:09 GMT 2012


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.





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121230/7b1ab13d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 00000928.3.00-All.vcf.gz.vex_37053338.vcf
Type: text/directory
Size: 6897 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121230/7b1ab13d/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121230/7b1ab13d/attachment-0001.html>


More information about the Dev mailing list