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plagnollab / DNASeq_pipeline

Pipeline in place at the UGI for DNA level analysis
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Get Picard CalculateHsMetrics working on BAM files. #23

Open pontikos opened 9 years ago

pontikos commented 9 years ago

See output below. Looks like target BED file needs a SAM header: http://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html

[rmhanpo@cooper:~/IBDAJE/Macrogen]$ /share/apps/jdk1.7.0_45/jre/bin/java -jar /cluster/project8/vyp/vincent/Software/picard-tools-1.100//CalculateHsMetrics.jar R=/scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta INPUT=OFG/align/data//OFG-01_sorted_unique.bam OUTPUT=OFG/hstmetrics/data//OFG-01_depth.txt BAIT_INTERVALS=/goon2/project99/IBDAJE_raw/BGI/nochr_target_region.bed TARGET_INTERVALS=/goon2/project99/IBDAJE_raw/BGI/nochr_target_region.bed
[Sat Jan 24 15:10:54 GMT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/goon2/project99/IBDAJE_raw/BGI/nochr_target_region.bed TARGET_INTERVALS=/goon2/project99/IBDAJE_raw/BGI/nochr_target_region.bed INPUT=OFG/align/data/OFG-01_sorted_unique.bam OUTPUT=OFG/hstmetrics/data/OFG-01_depth.txt REFERENCE_SEQUENCE=/scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta    METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sat Jan 24 15:10:54 GMT 2015] Executing as rmhanpo@cooper.local on Linux 2.6.18-371.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18; Picard version: 1.100(1571)
[Sat Jan 24 15:10:54 GMT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1012400128
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: Interval list file must contain header.
        at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:193)
        at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:169)
        at net.sf.picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:98)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:74)