#----------------------------------# # ENSEMBL VARIANT EFFECT PREDICTOR # #----------------------------------# version 2.7 By Will McLaren (wm2@ebi.ac.uk) Configuration options: #or allow_non_variant 1 buffer_size 50000 cache 1 canonical 1 ccds 1 check_alleles 1 check_existing 1 check_svs 1 chunk_size 500kb config vep_human.ini core_type core custom /ReferenceData/vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact /ReferenceData/vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact dir /ReferenceData/vep_cache/ domains 1 force_overwrite 1 fork 10 gmaf 1 hgnc 1 host ensembldb.ensembl.org individual all input_file OGT-SHROOM3-recalBams_All_BOTH.vcf numbers 1 output_file OGT-SHROOM3-recalBams_All_BOTH.vcf plugin OGT_pTranscripts OGT_Grantham Blosum62 Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b Carol polyphen b port 5306 protein 1 regulatory 1 sift b species homo_sapiens terms display toplevel_dir /ReferenceData/vep_cache/ vcf 1 verbose 1 xref_refseq 1 -------------------- Will only load v69 databases Species 'homo_sapiens' loaded from database 'homo_sapiens_core_69_37' Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_69_37' Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_69_37' Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_69_37' Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_69_37' homo_sapiens_variation_69_37 loaded homo_sapiens_funcgen_69_37 loaded Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara databases will be ignored: ensembl_compara_69 ensembl_ancestral_69 loaded ensembl_ontology_69 loaded 2012-11-27 13:40:36 - Connected to core version 69 database and variation version 69 database 2012-11-27 13:40:36 - Read existing cache info 2012-11-27 13:40:36 - Loaded plugin: OGT_pTranscripts 2012-11-27 13:40:36 - Loaded plugin: OGT_Grantham 2012-11-27 13:40:36 - Loaded plugin: Blosum62 2012-11-27 13:40:36 - Loaded plugin: Condel 2012-11-27 13:40:36 - Loaded plugin: Carol 2012-11-27 13:40:37 - Starting... 2012-11-27 13:40:37 - Detected format of input file as vcf 2012-11-27 13:40:40 - Read 50000 variants into buffer 2012-11-27 13:40:41 - Reading transcript data from cache and/or database [==================================================================================================================================================================================================] [ 100% ] 2012-11-27 13:41:56 - Retrieved 62622 transcripts (0 mem, 67995 cached, 0 DB, 5373 duplicates) 2012-11-27 13:41:56 - Reading regulatory data from cache and/or database [===========================================================================================================================================================> ] [ 80% ]^[==================================================================================================================================================================================================] [ 100% ] 2012-11-27 13:43:54 - Retrieved 337684 regulatory features (0 mem, 337778 cached, 0 DB, 94 duplicates) 2012-11-27 13:43:55 - Calculating consequences 2012-11-27 13:48:44 - Retrieved 85 custom annotations (61 dbsnp135, 24 Somatic) [========================================================================================> ] [ 46% ]2012-11-27 13:58:13 - Retrieved 29 custom annotations (20 dbsnp135, 9 Somatic) [===========================================================================> ] [ 39% ]2012-11-27 13:58:48 - Retrieved 164 custom annotations (144 dbsnp135, 20 Somatic) [===============================================================================================================================> ] [ 66% ]2012-11-27 14:04:27 - Retrieved 8 custom annotations (7 dbsnp135, 1 Somatic) [================================================================================================> ] [ 50% ]2012-11-27 14:04:40 - Retrieved 114 custom annotations (85 dbsnp135, 29 Somatic) [===================================================================================================================> ] [ 60% ]2012-11-27 14:05:20 - Retrieved 112 custom annotations (76 dbsnp135, 36 Somatic) [====================================================================================================================================================================> ] [ 85% ]2012-11-27 14:09:35 - Retrieved 155 custom annotations (102 dbsnp135, 53 Somatic) [====================================================================================================================================================> ] [ 77% ]2012-11-27 14:10:43 - Retrieved 84 custom annotations (50 dbsnp135, 34 Somatic) [============================================================================================================================================================================> ] [ 89% ]2012-11-27 14:12:13 - Retrieved 24 custom annotations (23 dbsnp135, 1 Somatic) [===================================================================================================================================================================================> ] [ 92% ]2012-11-27 14:14:42 - Retrieved 190 custom annotations (108 dbsnp135, 82 Somatic) [===================================================================================================================================================================> ] [ 84% ]2012-11-27 14:16:16 - Retrieved 136 custom annotations (79 dbsnp135, 57 Somatic) [======================================================================================================================================================================> ] [ 86% ]2012-11-27 14:17:36 - Retrieved 112 custom annotations (70 dbsnp135, 42 Somatic) [=========================================================================================================================================================================================> ] [ 96% ]2012-11-27 14:17:58 - Retrieved 10 custom annotations (8 dbsnp135, 2 Somatic) [===========================================================================================================================================================================> ] [ 88% ]2012-11-27 14:19:56 - Retrieved 123 custom annotations (87 dbsnp135, 36 Somatic) [===============================================================================================================================================================================================> ] [ 99% ]2012-11-27 14:22:55 - Retrieved 8 custom annotations (3 dbsnp135, 5 Somatic) [==================================================================================================================================================================================================] [ 100% ] 2012-11-27 14:23:08 - Writing output 2012-11-27 14:23:11 - Processed 50000 total variants (20 vars/sec, 20 vars/sec total) 2012-11-27 14:23:14 - Read 50000 variants into buffer 2012-11-27 14:23:18 - Reading transcript data from cache and/or database [==================================================================================================================================================================================================] [ 100% ] 2012-11-27 14:25:25 - Retrieved 58467 transcripts (6 mem, 63328 cached, 0 DB, 4867 duplicates) 2012-11-27 14:25:25 - Reading regulatory data from cache and/or database [==================================================================================================================================================================================================] [ 100% ] 2012-11-27 14:27:23 - Retrieved 303897 regulatory features (151 mem, 303838 cached, 0 DB, 92 duplicates) 2012-11-27 14:27:24 - Calculating consequences 2012-11-27 14:40:23 - Retrieved 54 custom annotations (27 dbsnp135, 27 Somatic) [========================> ] [ 13% ]2012-11-27 14:42:01 - Retrieved 39 custom annotations (25 dbsnp135, 14 Somatic) [=============================================> ] [ 24% ]2012-11-27 14:42:23 - Retrieved 72 custom annotations (44 dbsnp135, 28 Somatic) [====================================================================> ] [ 36% ]2012-11-27 14:42:56 - Retrieved 81 custom annotations (53 dbsnp135, 28 Somatic) [==========================================================================================> ] [ 47% ]2012-11-27 14:44:09 - Retrieved 113 custom annotations (72 dbsnp135, 41 Somatic) [=============================================================================================================> ] [ 57% ]2012-11-27 14:45:09 - Retrieved 27 custom annotations (20 dbsnp135, 7 Somatic) [===================================================================================================> ] [ 52% ]2012-11-27 14:45:47 - Retrieved 131 custom annotations (92 dbsnp135, 39 Somatic) [========================================================================================================================================> ] [ 71% ]2012-11-27 14:46:16 - Retrieved 61 custom annotations (50 dbsnp135, 11 Somatic) [=================================================================================================================================================================> ] [ 83% ]2012-11-27 14:46:52 - Retrieved 3 custom annotations (2 dbsnp135, 1 Somatic) [=========================================================================================================================================> ] [ 71% ]2012-11-27 14:47:00 - Retrieved 182 custom annotations (115 dbsnp135, 67 Somatic) [==============================================================================================================================================> ] [ 74% ] ERROR: Forked process failed 4wNHx8fHx8fHx8fCxUfEVOU0cwMDAwMDA5NTM3MHxFTlNUMDAwMDA0ODg2ODV8VHJh bnNjcmlwdHxJTlRST05JQyZXSVRISU5fTk9OX0NPRElOR19HRU5FfHx8fHx8cnMyMjMzNTAyfHx8 My80fFNIMkQzQ3xTUlIzMzA0NDF8fHx8fG5zdjQ4MjIzMyZuc3Y4MTc0NzAmbnN2NTMyNDAzJm5z djQ5MTg1OSZuc3Y1MzI0MDQmbnN2NTMyNDA2Jm5zdjQ5ODA1NCZuc3Y1Mjk1NzEmbnN2NTMyNDM0 Jm5zdjUyOTYwMCZuc3Y4Njg5NjYmbnN2NTMxNjM3Jm5zdjUyOTQ0NiZuc3Y4OTM4NTkmbnN2ODkz ODYwJm5zdjg5Mzg2NSZuc3Y4OTM4NjcmbnN2ODkzODY4Jm5zdjg5Mzg2OSZuc3Y0NjY1NzEmbnN2 ODkzODcwJm5zdjg5Mzg3MSZuc3Y0NzEzMjMmbnN2NDY2NTczJm5zdjQ2NjU3NCZuc3Y4MjUwOTR8 fHx8fFQ6MC4wNHx8fHx8fHx8fCxUfEVOU0cwMDAwMDA5NTM3MHxFTlNUMDAwMDAzMTQ4MzB8VHJh bnNjcmlwdHxJTlRST05JQ3x8fHx8fHJzMjIzMzUwMnxOTV8xNzA2MDAuMnx8NC8xMXxTSDJEM0N8 U1JSMzMwNDQxfHx8fHxuc3Y0ODIyMzMmbnN2ODE3NDcwJm5zdjUzMjQwMyZuc3Y0OTE4NTkmbnN2 NTMyNDA0Jm5zdjUzMjQwNiZuc3Y0OTgwNTQmbnN2NTI5NTcxJm5zdjUzMjQzNCZuc3Y1Mjk2MDAm bnN2ODY4OTY2Jm5zdjUzMTYzNyZuc3Y1Mjk0NDYmbnN2ODkzODU5Jm5zdjg5Mzg2MCZuc3Y4OTM4 NjUmbnN2ODkzODY3Jm5zdjg5Mzg2OCZuc3Y4OTM4NjkmbnN2NDY2NTcxJm5zdjg5Mzg3MCZuc3Y4 OTM4NzEmbnN2NDcxMzIzJm5zdjQ2NjU3MyZuc3Y0NjY1NzQmbnN2ODI1MDk0fHxZRVN8fHxUOjAu MDR8RU5TUDAwMDAwMzE3ODE3fHxDQ0RTNjg3Ny4xfHx8fHx8LFR8RU5TRzAwMDAwMDk1MzcwfEVO U1QwMDAwMDQxNDM4MHxUcmFuc2NyaXB0fElOVFJPTklDfHx8fHx8cnMyMjMzNTAyfHx8Mi8yfFNI MkQzQ3xTUlIzMzA0NDF8fHx8fG5zdjQ4MjIzMyZuc3Y4MTc0NzAmbnN2NTMyNDAzJm5zdjQ5MTg1 OSZuc3Y1MzI0MDQmbnN2NTMyNDA2Jm5zdjQ5ODA1NCZuc3Y1Mjk1NzEmbnN2NTMyNDM0Jm5zdjUy OTYwMCZuc3Y4Njg5NjYmbnN2NTMxNjM3Jm5zdjUyOTQ0NiZuc3Y4OTM4NTkmbnN2ODkzODYwJm5z djg5Mzg2NSZuc3Y4OTM4NjcmbnN2ODkzODY4Jm5zdjg5Mzg2OSZuc3Y0NjY1NzEmbnN2ODkzODcw Jm5zdjg5Mzg3MSZuc3Y0NzEzMjMmbnN2NDY2NTczJm5zdjQ2NjU3NCZuc3Y4MjUwOTR8fHx8fFQ6 MC4wNHxFTlNQMDAwMDA0MTM3NjB8fHx8fHx8fCxUfEVOU0cwMDAwMDA5NTM3MHxFTlNUMDAwMDA0 NzM1MzV8VHJhbnNjcmlwdHxJTlRST05JQyZXSVRISU5fTk9OX0NPRElOR19HRU5FfHx8fHx8cnMy MjMzNTAyfHx8Mi83fFNIMkQzQ3xTUlIzMzA0NDF8fHx8fG5zdjQ4MjIzMyZuc3Y4MTc0NzAmbnN2 NTMyNDAzJm5zdjQ5MTg1OSZuc3Y1MzI0MDQmbnN2NTMyNDA2Jm5zdjQ5ODA1NCZuc3Y1Mjk1NzEm bnN2NTMyNDM0Jm5zdjUyOTYwMCZuc3Y4Njg5NjYmbnN2NTMxNjM3Jm5zdjUyOTQ0NiZuc3Y4OTM4 NTkmbnN2ODkzODYwJm5zdjg5Mzg2NSZuc3Y4OTM4NjcmbnN2ODkzODY4Jm5zdjg5Mzg2OSZuc3Y0 NjY1NzEmbnN2ODkzODcwJm5zdjg5Mzg3MSZuc3Y0NzEzMjMmbnN2NDY2NTczJm5zdjQ2NjU3NCZu c3Y4MjUwOTR8fHx8fFQ6MC4wNHx8fHx8fHx8fCxUfEVOU0cwMDAwMDA5NTM3MHxFTlNUMDAwMDAz NzMyNzR8VHJhbnNjcmlwdHxJTlRST05JQ3x8fHx8fHJzMjIzMzUwMnxOTV8wMDExNDI1MzQuMXx8 Mi85fFNIMkQzQ3xTUlIzMzA0NDF8fHx8fG5zdjQ4MjIzMyZuc3Y4MTc0NzAmbnN2NTMyNDAzJm5z djQ5MTg1OSZuc3Y1MzI0MDQmbnN2NTMyNDA2Jm5zdjQ5ODA1NCZuc3Y1Mjk1NzEmbnN2NTMyNDM0 Jm5zdjUyOTYwMCZuc3Y4Njg5NjYmbnN2NTMxNjM3Jm5zdjUyOTQ0NiZuc3Y4OTM4NTkmbnN2ODkz ODYwJm5zdjg5Mzg2NSZuc3Y4OTM4NjcmbnN2ODkzODY4Jm5zdjg5Mzg2OSZuc3Y0NjY1NzEmbnN2 ODkzODcwJm5zdjg5Mzg3MSZuc3Y0NzEzMjMmbnN2NDY2NTczJm5zdjQ2NjU3NCZuc3Y4MjUwOTR8 fHx8fFQ6MC4wNHxFTlNQMDAwMDAzNjIzNzF8fENDRFM0ODAyNy4xfHx8fHx8LFR8RU5TRzAwMDAw MDk1MzcwfEVOU1QwMDAwMDQ2NDIzOXxUcmFuc2NyaXB0fElOVFJPTklDJldJVEhJTl9OT05fQ09E SU5HX0dFTkV8fHx8fHxyczIyMzM1MDJ8fHwzLzV8U0gyRDNDfFNSUjMzMDQ0MXx8fHx8bnN2NDgy MjMzJm5zdjgxNzQ3MCZuc3Y1MzI0MDMmbnN2NDkxODU5Jm5zdjUzMjQwNCZuc3Y1MzI0MDYmbnN2 NDk4MDU0Jm5zdjUyOTU3MSZuc3Y1MzI0MzQmbnN2NTI5NjAwJm5zdjg2ODk2NiZuc3Y1MzE2Mzcm bnN2NTI5NDQ2Jm5zdjg5Mzg1OSZuc3Y4OTM4NjAmbnN2ODkzODY1Jm5zdjg5Mzg2NyZuc3Y4OTM4 NjgmbnN2ODkzODY5Jm5zdjQ2NjU3MSZuc3Y4OTM4NzAmbnN2ODkzODcxJm5zdjQ3MTMyMyZuc3Y0 NjY1NzMmbnN2NDY2NTc0Jm5zdjgyNTA5NHx8fHx8VDowLjA0fHx8fHx8fHx8LFR8RU5TRzAwMDAw MDk1MzcwfEVOU1QwMDAwMDM3MzI3NnxUcmFuc2NyaXB0fElOVFJPTklDfHx8fHx8cnMyMjMzNTAy fE5NXzAwMTI1MjMzNC4xfHwzLzEwfFNIMkQzQ3xTUlIzMzA0NDF8fHx8fG5zdjQ4MjIzMyZuc3Y4 MTc0NzAmbnN2NTMyNDAzJm5zdjQ5MTg1OSZuc3Y1MzI0MDQmbnN2NTMyNDA2Jm5zdjQ5ODA1NCZu c3Y1Mjk1NzEmbnN2NTMyNDM0Jm5zdjUyOTYwMCZuc3Y4Njg5NjYmbnN2NTMxNjM3Jm5zdjUyOTQ0 NiZuc3Y4OTM4NTkmbnN2ODkzODYwJm5zdjg5Mzg2NSZuc3Y4OTM4NjcmbnN2ODkzODY4Jm5zdjg5 Mzg2OSZuc3Y0NjY1NzEmbnN2ODkzODcwJm5zdjg5Mzg3MSZuc3Y0NzEzMjMmbnN2NDY2NTczJm5z djQ2NjU3NCZuc3Y4MjUwOTR8fHx8fFQ6MC4wNHxFTlNQMDAwMDAzNjIzNzN8fHx8fHx8fAlHVDpB RDpEUDpHUTpQTAkwLzE6MjEsMjE6NDM6OTk6Njc5LDAsNTkw