GATK4运行BaseRecalibrator时报错

elaine2017

命令如下：
[mw_shl_code=shell,true]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[/mw_shl_code]

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？

zhou945876833

你用的vcf文件都构建了索引文件么？没有vcf.idx文件你就用GATK的IndexFeatureFile构建一下。
你报错的信息给的不全面，至少我看不到全部。

elaine2017

zhou945876833 发表于 2018-5-16 15:30
你用的vcf文件都构建了索引文件么？没有vcf.idx文件你就用GATK的IndexFeatureFile构建一下。
你报错的信息 ...

错误的地方就是你说的这个，昨天检查了一下，发现vcf文件的索引文件大小都是0 ，原来直接用GATK的IndexFeatureFile构建就可以了吗，我试过bcftools index，不过没成功，vcf必须得是bgzip压缩的，然后我又用bgzip压缩，也没成功，想问问这个gatk的IndexFeatureFile对文件有要求吗

zhou945876833

elaine2017 发表于 2018-5-17 11:34
错误的地方就是你说的这个，昨天检查了一下，发现vcf文件的索引文件大小都是0 ，原来直接用GATK的IndexFe ...

是的直接用GATK的IndexFeatureFile构建index