ensembl variant effect predictor

Question

[abdulbenissa]

Hello everyone

Am trying to run the perl variant_effect_predictor on the ensembl virtual machine and getting this error bellow when I run the my vcf files, but when when I try to run the example.vcf is totally fine and I get all the result !! can anyone help

ensembl@ensembl:~/ensembl-api-folder-82/ensembl-tools/scripts/variant_effect_predictor$ perl variant_effect_predictor.pl --input_file ~/Shared\ Folders/OutputAnalysis/TSVC_variants_IonXpress_048.vcf --cache --output_file 12.vcf
2016-02-13 15:11:40 - Read existing cache info
2016-02-13 15:11:41 - Starting...
2016-02-13 15:11:41 - Detected format of input file as vcf
2016-02-13 15:11:41 - Read 494 variants into buffer
2016-02-13 15:11:41 - Reading transcript data from cache and/or database
[================================================================>                                                                       ]   [ 48% ]

ERROR: Cannot allocate memory at /home/ensembl/ensembl-api-folder/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4978, <GEN0> line 592.

Answer 1

[abascalfederico]

Try changing the buffer_size to reduce memory usage

--buffer_size [number]

Sets the internal buffer size, corresponding to the number of variations that are read in to memory simultaneously. Set this lower to use less memory at the expense of longer run time, and higher to use more memory with a faster run time. Default = 5000

[abdulbenissa]

Thanks, it works well now!