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Mutect2 problems on nct parameter

mpolanompolano ItalyMember

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 
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
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?


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