Question: ensembl variant effect predictor
0
gravatar for abdulbenissa
3.3 years ago by
Saudi Arabia
abdulbenissa0 wrote:

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.

ADD COMMENTlink modified 3.3 years ago by abascalfederico1.1k • written 3.3 years ago by abdulbenissa0
1
gravatar for abascalfederico
3.3 years ago by
abascalfederico1.1k
Spain
abascalfederico1.1k wrote:

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
 
ADD COMMENTlink written 3.3 years ago by abascalfederico1.1k

Thanks works well now !! 

ADD REPLYlink written 3.3 years ago by abdulbenissa0
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