GATK报错信息汇总
2019-05-31 本文已影响0人
晓佥
GATK最容易出错的地方，个人认为是VQSR这一步，其他的步骤倒是好说，基本上走流程都可以走下来，VQSR这一步几乎对于每一个数据集，所使用的参数都会多少有一些差别，所以出错的概率会大一些，我把我遇到的主要错误，及其排错方法，罗列出来，希望能够帮助到一些人。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions [http://www.broadinstitute.org/gatk](http://www.broadinstitute.org/gatk)
##### ERROR
##### ERROR MESSAGE: Unable to retrieve result
##### ERROR ------------------------------------------------------------------------------------------
这是因为设置的VQSR这一步，numBad这个参数设置太大了，调低一些就可以了。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
##### 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](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: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --numBad 3000, for example).
##### ERROR ------------------------------------------------------------------------------------------
这是因为设置的numBad数量太小了
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
##### 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](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: Lexicographically sorted human genome sequence detected in reads.
##### ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.
##### ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.
##### ERROR You can use the ReorderSam utility to fix this problem:[http://gatkforums.broadinstitute.org/discussion/58/companion-utilities-reordersam](http://gatkforums.broadinstitute.org/discussion/58/companion-utilities-reordersam)
##### ERROR reads contigs = [chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17_ctg5_hap1, chr17, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr1, chr1_gl000191_random, chr1_gl000192_random, chr20, chr21, chr21_gl000210_random, chr22, chr2, chr3, chr4_ctg9_hap1, chr4, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7, chr7_gl000195_random, chr8, chr8_gl000196_random, chr8_gl000197_random, chr9, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chrM, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249, chrX, chrY]
这是因为用于callsnp的sam文件没有按照染色体1,2,3,4....22，X,Y,M的顺序排序，可以手动更改或者使用ReorderSam功能修改 http://gatkforums.broadinstitute.org/discussion/58/companion-utilities-reordersam
注意：hardfilter的时候不能filter format里面的注释
在对vcf文件VariantAnnotator进行重新注释的时候 -A参数 后面跟的注释必须写全称！！！
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Exception in thread "main" java.lang.UnsupportedClassVersionError:
org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$000(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit.
这时候就是java版本不对，如果是GATK2.7以后的版本，需要下载1.7以后版本的java
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Input files /ifs1/ST_POP/PMO/Mongolian_POP/lantianming/Mongolian_tianjin_vcf/final.vcf and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR /ifs1/ST_POP/PMO/Mongolian_POP/lantianming/Mongolian_tianjin_vcf/final.vcf contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
这个是应为所用的参考序列和vcf序列有冲突，也就是说如果vcf文件中是chr1-chr22，参考序列也应该是chr1-chr22，如果参考序列是chr1-chr22+chrX+chrY+chrM的话，就会报这个错误
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Bad input: Values for SnpEff annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See [http://gatkforums.broadinstitute.org/discussion/49/using-variant-annotator](http://gatkforums.broadinstitute.org/discussion/49/using-variant-annotator)
##### ERROR ------------------------------------------------------------------------------------------
这个说明你做VQSR的时候，在-an参数所添加的某一个注释信息在vcf文件里面没有，这时候有两种选择，一种是用variant-annotator这个工具在vcf文件中加上这个注释，另一种是把那个-an参数去掉。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/hapmap_3.3.hg19.vcf.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system.
##### ERROR ------------------------------------------------------------------------------------------
这个错误说实话我也不是很清楚，可能是不能同时调用bundle里的一些文件，如果同时调用同一个文件，可能就会出现这个错误，解决方法可以这样试一下：就是如果多个任务都需要调用某同一文件的时候，让任务顺序运行，而不要并行操作。不妨试一下。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Input files input and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR contig input = chrM / 16569
##### ERROR contig reference = chrM / 16571.
##### ERROR input contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
这个说明你的输入文件（原始VCF文件）构建的索引文件（.idx）所用的参考基因组，和，你现在所用的参考基因组不一致。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Input files input and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR input contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]
##### ERROR ------------------------------------------------------------------------------------------
这个说明你的输入文件（原始VCF文件）构建的索引文件（.idx）所用的参考基因组，和，你现在所用的参考基因组不一致。跟上面的错误一样，只不过这次不是因为某一条染色体长度不一致，而是染色体的排序不一致。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Input files mills and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR contig mills = chrM / 16571
##### ERROR contig reference = chrM / 16569.
##### ERROR mills contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
##### ERROR ------------------------------------------------------------------------------------------
这个错误说明你的输入文件（原始VCF文件）构建的索引文件（.idx）所用的参考基因组，和，你现在所用的knows选项所指定的文件中的索引文件构建所用的参考序列不一致。
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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
##### 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](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: Bad input: Found annotations with zero variance. They must be excluded before proceeding.
##### ERROR ------------------------------------------------------------------------------------------
这个错误提示在做ApplyRecalibration的时候，所使用的一些tags也就是annotations是不适用的，应该把这些注释去掉，这个错误一般会在indel里面出现，因为用于在SNP calling中所使用的一些注释信息在INDEL calling中不可用
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