【无标题】gatk FilterMutectCalls输出结果为空，报错Error: the last column in header row should start with ‘Otherinf

提交任务跑时报错Error: the last column in header row should start with 'Otherinfo'；

报错原因：mutect2得到的vcf文件中有一行或者多行的列数和其他行不一样；

解决办法：再运行一次，看看到底是哪一行，gatk FilterMutectCalls输出结果中有指示哪一行，但需要非常仔细看才看得出来，如下图的121473这一行。

(base) [*]$ $gatk FilterMutectCalls -R $gatkgenomeFasta -V $output/${id}P_mutect2.vcf -O $output/${id}P_somatic.vcf
Using GATK jar ./software/gatk-4.2.4.1/gatk-package-4.2.4.1-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar ./software/gatk-4.2.4.1/gatk-package-4.2.4.1-local.jar FilterMutectCalls -R ./GATK_hg38_v0_Homo_sapiens_assembly38.fasta -V ./p473P_mutect2.vcf -O ./p473P_somatic.vcf
11:27:11.455 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:./software/gatk-4.2.4.1/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 04, 2023 11:27:11 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:27:11.716 INFO  FilterMutectCalls - ------------------------------------------------------------
11:27:11.717 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.2.4.1
11:27:11.717 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
11:27:11.717 INFO  FilterMutectCalls - Executing as yangsuqin@cpu05 on Linux v3.10.0-957.el7.x86_64 amd64
11:27:11.718 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-b13
11:27:11.718 INFO  FilterMutectCalls - Start Date/Time: June 4, 2023 11:27:11 AM CST
11:27:11.718 INFO  FilterMutectCalls - ------------------------------------------------------------
11:27:11.718 INFO  FilterMutectCalls - ------------------------------------------------------------
11:27:11.719 INFO  FilterMutectCalls - HTSJDK Version: 2.24.1
11:27:11.719 INFO  FilterMutectCalls - Picard Version: 2.25.4
11:27:11.719 INFO  FilterMutectCalls - Built for Spark Version: 2.4.5
11:27:11.719 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:27:11.719 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:27:11.719 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:27:11.720 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:27:11.720 INFO  FilterMutectCalls - Deflater: IntelDeflater
11:27:11.720 INFO  FilterMutectCalls - Inflater: IntelInflater
11:27:11.720 INFO  FilterMutectCalls - GCS max retries/reopens: 20
11:27:11.720 INFO  FilterMutectCalls - Requester pays: disabled
11:27:11.721 INFO  FilterMutectCalls - Initializing engine
11:27:12.496 INFO  FeatureManager - Using codec VCFCodec to read file file:./p473P_mutect2.vcf
11:27:13.052 INFO  FilterMutectCalls - Done initializing engine
11:27:13.250 INFO  ProgressMeter - Starting traversal
11:27:13.250 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
11:27:13.251 INFO  FilterMutectCalls - Starting pass 0 through the variants
11:27:23.254 INFO  ProgressMeter -       chr10:42078104              0.2                 53000         317968.2
11:27:28.615 INFO  FilterMutectCalls - Shutting down engine
[June 4, 2023 11:27:28 AM CST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=2076049408
htsjdk.tribble.TribbleException: Line 121473: there aren't enough columns for line T=6;MBQ=33,35;MFRL=465,463;MMQ=36,40;MPOS=18;NALOD=-7.184e+00;NLOD=12.04;POPAF=6.00;TLOD=77.04	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:90,4:0.053:94:38,2:47,2:90,4:62,28,3,1	0/1:98,28:0.226:126:51,15:40,13:100,28:80,18,18,10 (we expected 9 tokens, and saw 4 ), for input source: ./p473P_mutect2.vcf
	at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:381)
	at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:328)
	at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:48)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37)
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:375)
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:354)
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:315)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
	at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)
	at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)

 解决办法：在mutect2得到的vcf文件找到这一行附近发几行，看看到底是哪一行的的列数和其他的不一样，删除该行重新跑即可。

例子如下：

cat p430P_mutect2.vcf -n |head -n 118280 | tail -n +118270#发现第118278行不是chr开头的，删除掉这一行
sed -i '118278d' p430P_mutect2.vcf

缺点：需要对每一个样本都进行这样的测试