Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

picard error :picard.analysis.directed.CalculateHsMetrics

yaoqianlanyaoqianlan china shanghaiMember

${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar CleanSam VALIDATION_STRINGENCY=SILENT INPUT=${EXOME_RESULT_DIR}/2-Mapping/BWA/${SAMPLE_ID}_output.bam OUTPUT=picard/${SAMPLE_ID}_output.fix.bam
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar FixMateInformation VALIDATION_STRINGENCY=SILENT INPUT=picard/${SAMPLE_ID}_output.fix.bam OUTPUT=picard/${SAMPLE_ID}_output.tmp.bam TMP_DIR=picard/temp
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar AddOrReplaceReadGroups VALIDATION_STRINGENCY=SILENT INPUT=picard/${SAMPLE_ID}_output.fix.bam OUTPUT=picard/${SAMPLE_ID}_output.fix.rg.bam LB=test PL=Illumina PU=test1 SM=${SAMPLE_ID}
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar SortSam VALIDATION_STRINGENCY=SILENT INPUT=picard/${SAMPLE_ID}_output.fix.rg.bam OUTPUT=picard/${SAMPLE_ID}_output.fix.rg.sort.bam SORT_ORDER=coordinate TMP_DIR=picard/temp
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar MarkDuplicates VALIDATION_STRINGENCY=SILENT INPUT=picard/${SAMPLE_ID}_output.fix.rg.sort.bam OUTPUT=picard/${SAMPLE_ID}_output.fix.rg.sort.mkdup.bam METRICS_FILE=picard/${SAMPLE_ID}.mkdup.metrics
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar BuildBamIndex VALIDATION_STRINGENCY=SILENT INPUT=picard/${SAMPLE_ID}_output.fix.rg.sort.mkdup.bam
${JAVA_HOME}/java -jar ${Picard_PATH}/picard.jar CalculateHsMetrics VALIDATION_STRINGENCY=SILENT BAIT_INTERVALS=${CAPTURE_TARGET} TARGET_INTERVALS=${CAPTURE_TARGET} INPUT=picard/${SAMPLE_ID}_output.fix.rg.sort.mkdup.bam OUTPUT=picard/${SAMPLE_ID}.mapping.metrics
${R_PATH}/Rscript --no-save script/mapping.graphics.R picard/${SAMPLE_ID}.mapping.metrics

[Mon Aug 01 10:38:41 CST 2016] picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=[/export4/xielu_group/data120/sibs/fdyu/index/PicardIntervalFile/list.interval_list_hg38] TARGET_INTERVALS=[/export4/xielu_group/data120/sibs/fdyu/index/PicardIntervalFile/list.interval_list_hg38] INPUT=picard/Sample_20160526_107B_output.fix.rg.sort.mkdup.bam OUTPUT=picard/Sample_20160526_107B.mapping.metrics VALIDATION_STRINGENCY=SILENT MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 SAMPLE_SIZE=10000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Mon Aug 01 10:38:41 CST 2016] Executing as [email protected] on Linux 2.6.32-279.14.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: 2.5.0(2c370988aefe41f579920c8a6a678a201c5261c1_1466708365)
INFO 2016-08-01 10:38:48 CalculateHsMetrics Processed 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: 10:30,693,354
INFO 2016-08-01 10:38:51 CalculateHsMetrics Processed 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: 10:47,544,403
[Mon Aug 01 10:38:53 CST 2016] picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=1908932608
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.acceptRecord(TargetMetricsCollector.java:534)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.acceptRecord(TargetMetricsCollector.java:349)
at picard.metrics.MultiLevelCollector$AllReadsDistributor.acceptRecord(MultiLevelCollector.java:192)
at picard.metrics.MultiLevelCollector.acceptRecord(MultiLevelCollector.java:315)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:146)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Fatal error: you must specify '--save', '--no-save' or '--vanilla'

please tell me what is going wrong? what should i do. Thank you !

qianlanyao

Answers

Sign In or Register to comment.