命令如下:
[Shell] 纯文本查看 复制代码 java -jar ~/tools/gatk-4.0.3.0/gatk-package-4.0.3.0-local.jar BaseRecalibrator \
-R ~/project/ref/hg38/Homo_sapiens_assembly38.fasta \
-I N1.sorted.MarkDuplicates.bam -L ../aml_hg38.probe.bed -ip 90 \
--known-sites ~/tools/GATK/1000G_omni2.5.hg38.vcf \
--known-sites ~/tools/GATK/1000G_phase1.snps.high_confidence.hg38.vcf \
--known-sites ~/tools/GATK/dbsnp_146.hg38.vcf \
--known-sites ~/tools/GATK/hapmap_3.3.hg38.vcf \
--known-sites ~/tools/GATK/Mills_and_1000G_gold_standard.indels.hg38.vcf \
-O $fname.realn.recal
错误信息如下:
14:41:18.808 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/public/home/lijie/tools/gatk-4.0.3.0/gatk-package-4.0.3.0-local.jar!/com/intel/
gkl/native/libgkl_compression.so
14:41:19.208 INFO BaseRecalibrator - ------------------------------------------------------------
14:41:19.208 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.0.3.0
14:41:19.208 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:41:19.209 INFO BaseRecalibrator - Executing as lijie@node2 on Linux v2.6.32-504.el6.x86_64 amd64
14:41:19.209 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_121-b15
14:41:19.210 INFO BaseRecalibrator - Start Date/Time: May 16, 2018 2:41:18 PM CST
14:41:19.210 INFO BaseRecalibrator - ------------------------------------------------------------
14:41:19.210 INFO BaseRecalibrator - ------------------------------------------------------------
14:41:19.210 INFO BaseRecalibrator - HTSJDK Version: 2.14.3
14:41:19.211 INFO BaseRecalibrator - Picard Version: 2.17.2
14:41:19.211 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:41:19.211 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:41:19.211 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:41:19.211 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:41:19.211 INFO BaseRecalibrator - Deflater: IntelDeflater
14:41:19.211 INFO BaseRecalibrator - Inflater: IntelInflater
14:41:19.211 INFO BaseRecalibrator - GCS max retries/reopens: 20
14:41:19.211 INFO BaseRecalibrator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/d
r_all_nio_fixes
14:41:19.212 INFO BaseRecalibrator - Initializing engine
14:41:20.500 INFO FeatureManager - Using codec VCFCodec to read file file:///public/home/lijie/tools/GATK/1000G_omni2.5.hg38.vcf
14:41:20.618 INFO BaseRecalibrator - Shutting down engine
[May 16, 2018 2:41:20 PM CST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1707081728
htsjdk.tribble.TribbleException: Problem detecting index type
at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:149)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:179)
at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:162)
at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:227)
at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:262)
at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:202)
at org.broadinstitute.hellbender.engine.FeatureManager.initializeFeatureSources(FeatureManager.java:182)
at org.broadinstitute.hellbender.engine.FeatureManager.<init>(FeatureManager.java:153)
at org.broadinstitute.hellbender.engine.ReadWalker.initializeFeatures(ReadWalker.java:73)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:558)
at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(ReadWalker.java:55)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:132)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
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)
Caused by: java.io.EOFException
at htsjdk.tribble.util.LittleEndianInputStream.readInt(LittleEndianInputStream.java:66)
at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:137)
... 16 more
请问这是哪里出问题了?
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