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Mutect2 problems on nct parameter
Dear All I use GAtk 3.6 an I sue Mutect2. I have a dell wiht 16 cpu with 50G of ram.
[[email protected]]$ java -version java version "1.8.0_101" Java(TM) SE Runtime Environment (build 1.8.0_101-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
I try many configuration of _Xmx (10,20 or without setting a value).
I use nct 4,6,10 but however it is very slow.
INFO 10:31:18,497 HelpFormatter - The Genome Analysis Toolkit (GA TK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 INFO 10:31:18,497 HelpFormatter - Copyright (c) 2010-2016 The Bro ad Institute INFO 10:31:18,497 HelpFormatter - For support and documentation g o to https://www.broadinstitute.org/gatk INFO 10:31:18,498 HelpFormatter - [Fri Mar 17 10:31:18 CET 2017] Executing on Linux 2.6.18-308.1.1.el5 amd64 INFO 10:31:18,498 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13 JdkDeflater INFO 10:31:18,502 HelpFormatter - Program Args: --analysis_type M uTect2 -dt NONE -baq OFF --validation_strictness LENIENT -nct 6 -- disable_auto_index_creation_and_locking_when_reading_rods --refere nce_sequence /illumina/software/database/database_2016/hg19_primar y.fa --dbsnp /illumina/software/Mutect_db/dbsnp_137.hg19.vcf.gz -- cosmic /illumina/software/database/b37_cosmic_v54_120711_mode.vcf --input_file:normal ALIGN/413/Coclean/414.sorted.dup.recal.cleaned .bam --input_file:tumor ALIGN/413/Coclean/413.sorted.dup.recal.cle aned.bam --out ALIGN/413/rawMuTect2/413_mutect2 -L /illumina/softw are/database/database_2016/TARGET/truseq-exome-targeted-regions-ma nifest-v1-2.bed -out_mode EMIT_ALL_SITES INFO 10:31:18,507 HelpFormatter - Executing as [email protected] -01.ilmn on Linux 2.6.18-308.1.1.el5 amd64; Java HotSpot(TM) 64-Bi t Server VM 1.8.0_101-b13.
the strange thing is they need more than 23 day for one sample of exome seq with 100X.
Could you please help me?