${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 fdyu@nc-1-1.local 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