[ensembl-dev] another VEP error in TranscriptVariationAllele.pm
Michael Yourshaw
myourshaw at ucla.edu
Mon Dec 31 20:14:42 GMT 2012
In Variant Effect Predictor 2.7 I get the following error when there is an amino acid insertion at a stop codon, which causes the program to stop:
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 877, <GEN1> line 5065.
The complaining line is:
elsif( (length($hgvs_notation->{alt}) > length($hgvs_notation->{ref}) ) &&
$hgvs_notation->{alt} =~ /$hgvs_notation->{ref}/ ) {
where $hgvs_notation->{alt} is “YPDSL” and $hgvs_notation->{ref} is “*”
The offending VCF is attached.
TERMINAL OUTPUT:
2012-12-31 12:10:07 - 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_37061804.vcf
no_progress 1
numbers 1
output_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37061804.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
--------------------
2012-12-31 12:10:07 - Connected to core version 69 database and variation version 69 database
2012-12-31 12:10:07 - Loaded plugin: vw
2012-12-31 12:10:07 - Loaded plugin: Condel
2012-12-31 12:10:07 - Loaded plugin: VCFCols
2012-12-31 12:10:07 - Fetching regulatory features for plugin: VCFCols
2012-12-31 12:10:07 - Loaded plugin: ExtraCols
2012-12-31 12:10:07 - Fetching regulatory features for plugin: ExtraCols
2012-12-31 12:10:07 - Loaded plugin: Consequences
2012-12-31 12:10:07 - Fetching regulatory features for plugin: Consequences
2012-12-31 12:10:09 - Loaded plugin: Conservation
2012-12-31 12:10:09 - Fetching regulatory features for plugin: Conservation
2012-12-31 12:10:09 - Starting...
2012-12-31 12:10:09 - Read 1 variants into buffer
2012-12-31 12:10:09 - Reading transcript data from cache and/or database
2012-12-31 12:10:09 - Retrieved 23 transcripts (0 mem, 0 cached, 23 DB, 0 duplicates)
2012-12-31 12:10:09 - Reading regulatory data from cache and/or database
2012-12-31 12:10:10 - Retrieved 3 regulatory features (0 mem, 0 cached, 3 DB, 0 duplicates)
2012-12-31 12:10:10 - Checking for existing variations
2012-12-31 12:10:10 - Checking for overlapping structural variations
2012-12-31 12:10:10 - Analyzing chromosome 3
2012-12-31 12:10:10 - Analyzing variants
2012-12-31 12:10:10 - Analyzing RegulatoryFeatures
2012-12-31 12:10:10 - Analyzing MotifFeatures
2012-12-31 12:10:10 - Calculating consequences
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 865, <GEN2> line 60.
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
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