Java虚拟机因堆大小增加而失败_Java_Jvm

Java虚拟机因堆大小增加而失败

java jvm

Java虚拟机因堆大小增加而失败,java,jvm,Java,Jvm,S0我试图运行的命令是 java -jar -Xmx290G /ibers/ernie/home/thh32/rumenISPG/GenomeAnalysisTK.jar -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || Hapl

S0我试图运行的命令是

java -jar -Xmx290G  /ibers/ernie/home/thh32/rumenISPG/GenomeAnalysisTK.jar  -T VariantFiltration -R Contigs_1.fa  -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf  --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQuality RankSum < -12.5 "  --filterName "testing_filter"  -o filtered_snps.vcf

是否有其他人遇到过此问题？如果是，您是否解决了此问题

哦，还有，万一人们想知道我为什么给这个程序这么多内存，而我没有，我得到了这个消息，这表明它需要更多的内存。这是一个100克大小的堆

INFO  09:55:57,953 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:57,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12 
INFO  09:55:57,956 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  09:55:57,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  09:55:57,961 HelpFormatter - Program Args: -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression QD < 2.0 || FS > 60.0 ||
 MQ < 40.0 || HaplotypeScore > 13.0 || MappingQuality RankSum < -12.5  --filterName testing_filter -o filtered_snps.vcf 
INFO  09:55:57,967 HelpFormatter - Executing as thh32@node011 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26. 
INFO  09:55:57,968 HelpFormatter - Date/Time: 2015/10/27 09:55:57 
INFO  09:55:57,968 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:57,969 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:58,474 GenomeAnalysisEngine - Strictness is SILENT 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.4-46-gbc02625): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program.  See the -Xmx JVM argument to adjust the maximum heap size provided to Java
##### ERROR ------------------------------------------------------------------------------------------

INFO 09:55:57953帮助格式化程序-------------------------------------------------------------------
信息09:55:57955 HelpFormatter-基因组分析工具包（GATK）v3.4-46-gbc02625，编译于2015/07/09 17:38:12
信息09:55:57956 HelpFormatter-版权所有（c）2010博德研究所
信息09:55:57956 HelpFormatter-有关支持和文档，请访问http://www.broadinstitute.org/gatk 
INFO 09:55:57961 HelpFormatter-程序参数：-T VariantFilter-R Contigs_1.fa-V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf--过滤器表达式QD<2.0 | FS>60.0||
MQ<40.0 | | |单倍型得分>13.0 | | |映射质量等级SUM<-12.5——筛选名称测试|筛选|筛选| snps.vcf
信息09:55:57967帮助格式化程序-作为执行thh32@node011在Linux 2.6.32-504.30.3.el6.x86_64 amd64上；Java HotSpot（TM）64位服务器VM 1.8.0_40-b26。
信息09:55:57968帮助格式化程序-日期/时间：2015/10/27 09:55:57
信息09:55:57968帮助格式化程序-------------------------------------------------------------------
信息09:55:57969帮助格式化程序-------------------------------------------------------------------
信息09:55:58474基因分析引擎-严格是无声的
#####错误------------------------------------------------------------------------------------------
#####错误发生用户错误（版本3.4-46-gbc02625）：
#####错误
#####错误这意味着命令中的一个或多个参数或输入不正确。
#####错误下面的错误消息告诉您问题所在。
#####错误
#####错误如果问题是无效参数，请查看联机文档指南
#####查看此工具允许的命令行参数时出错（或使用--help重新运行命令）。
#####错误
#####错误请访问我们的网站和论坛，获取详细的文档和问题解答
#####常见问题的错误http://www.broadinstitute.org/gatk
#####错误
#####错误请不要将此错误发布到GATK论坛，除非您真的试图自己修复它。
#####错误
#####错误消息：出现故障，因为您没有提供足够的内存来运行此程序。请参阅-Xmx JVM参数以调整提供给Java的最大堆大小
#####错误------------------------------------------------------------------------------------------

谢谢，

Tom

你确定你正在运行64位JVM吗？@sharonbn

Linux2.6.32-504.30.3.el6.x86_64 amd64；Java HotSpot（TM）64位服务器

消息说它无法分配大约9G，因此您可以尝试使用-Xmx250G。另外，可能还有另一个进程在运行，分配大量RAM？

free-h

为您提供了什么？我们使用qsub进行作业，因此我知道这些作业在达到堆限制后会失败，也因为我们使用qsub，我认为

free-h

不起作用。正确的语法是

-XX:-UseParallelGC

。注意冒号。

INFO  09:55:57,953 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:57,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12 
INFO  09:55:57,956 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  09:55:57,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  09:55:57,961 HelpFormatter - Program Args: -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression QD < 2.0 || FS > 60.0 ||
 MQ < 40.0 || HaplotypeScore > 13.0 || MappingQuality RankSum < -12.5  --filterName testing_filter -o filtered_snps.vcf 
INFO  09:55:57,967 HelpFormatter - Executing as thh32@node011 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26. 
INFO  09:55:57,968 HelpFormatter - Date/Time: 2015/10/27 09:55:57 
INFO  09:55:57,968 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:57,969 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  09:55:58,474 GenomeAnalysisEngine - Strictness is SILENT 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.4-46-gbc02625): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program.  See the -Xmx JVM argument to adjust the maximum heap size provided to Java
##### ERROR ------------------------------------------------------------------------------------------