[ensembl-dev] VEP script runtime errors

[Hardip Patel]

Dear all

I am trying to run vep script using local database and cache using the following command.

perl variant_effect_predictor.pl --output_file output.vep --species homo_sapiens --host localhost --user user --password password --port 1111 --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift b --force_overwrite --input_file input.vcf -skip_db_check


However, there are few warning thrown. Could somebody please let me know if these warnings are acceptable and will not affect the output in anyways?

First warning:
Use of qw(...) as parentheses is deprecated at /home/depressed/variant_effect_predictor/variant_effect_predictor.pl line 848.

I am guessing this is the result of using perl v14.2 and also guessing that this should not have any serious consequence at this stage.

Second warning is as follows:
2012-01-26 17:11:42 - Reading cached adaptor data
Use of uninitialized value in join or string at /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 3495.

Again guessing that this doesn't cascade into serious trouble while reporting results of the script.

However I am more concerned about following warnings (I get multiple of them).

Use of uninitialized value in sprintf at /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 932, <GEN0> line 315932.

Trying to debug the code indicated that vcf line responsible for these are (examples only out of many)

chr1	57005269	.	AACACA	AACA	217	.	INDEL;DP=25;VDB=0.0292;AF1=0.5;AC1=1;DP4=9,5,4,6;MQ=50;FQ=217;PV4=0.41,0.00046,1,0.38	GT:PL:DP:SP:GQ	0/1:255,0,255:24:4:99
chr1	61542770	.	GAGGGGAGAAGGGG	GAGGGGAGAAGGGGAGAAGGGG	106	.	INDEL;DP=23;VDB=0.0337;AF1=0.5;AC1=1;DP4=1,9,3,6;MQ=41;FQ=109;PV4=0.3,1,0,1	GT:PL:DP:SP:GQ	0/1:144,0,245:19:5:99

Any help on this matter is greatly appreciated.

Thanking you.

Kind regards


Hardip R. Patel, PhD
Post-doctoral Research Fellow

Genome Discovery Unit and RNA Biology Lab
Genome Biology Department
The John Curtin School of Medical Research
College of Medicine, Biology and Environment
The Australian National University
Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
Phone Number: (+61) 0449 180 715




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