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BAIT Interval and Target Interval file format issue.

vaibhav_kulkarnivaibhav_kulkarni Pune,IndiaMember Posts: 2

I'm trying to run CalculateHsMetrics with following command from Picard Tools

java -jar /tools/picard-tools-1.141/picard.jar CalculateHsMetrics \
BI=probe_cancer_panel_2.0.bed \
TI=target_cancer_panel_2.0.bed \
I=R1_edit3_8bp_TE030_fq-quality_checked_R2_edit3_8bp_TE030_fq-quality_checked__sort46.bam \
O=output

Getting Following STDOUT:

[Thu Feb 11 15:40:12 IST 2016] picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=[probe_cancer_panel_2.0.bed] TARGET_INTERVALS=[target_cancer_panel_2.0.bed] INPUT=R1_edit3_8bp_TE030_fq-quality_checked_R2_edit3_8bp_TE030_fq-quality_checked__sort46.bam OUTPUT=output 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 GA4GH_CLIENT_SECRETS=client_secrets.json
[Thu Feb 11 15:40:12 IST 2016] Executing as root@pts00256 on Linux 3.16.0-30-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15; Picard version: 1.141(8ece590411350163e7689e9e77aab8efcb622170_1447695087) IntelDeflater
[Thu Feb 11 15:40:12 IST 2016] picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: Interval list file must contain header.
at htsjdk.samtools.util.IntervalList.fromReader(IntervalList.java:436)
at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:381)
at htsjdk.samtools.util.IntervalList.fromFiles(IntervalList.java:410)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:85)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

I'm not able to understand "Interval list file must contain header."

"probe_cancer_panel_2.0.bed" file used as BAIT file, contents(first 10 lines) as follows :

chr1 17345282 17345332 SDHB|NM_003000_exon_0_0_chr1_17345225_r_1_1939010 1000 +
chr1 17345375 17345425 SDHB|NM_003000_exon_0_0_chr1_17345225_r_0_1939009 1000 -
chr1 17345486 17345536 SDHB|NM_003000_exon_0_0_chr1_17345225_r_1_1939010 1000 -
chr1 17345123 17345173 SDHB|NM_003000_exon_0_0_chr1_17345225_r_0_1939009 1000 +
chr1 17349254 17349304 SDHB|NM_003000_exon_1_0_chr1_17349103_r_0_2563050 1000 -
chr1 17349014 17349064 SDHB|NM_003000_exon_1_0_chr1_17349103_r_0_2563050 1000 +
chr1 17350378 17350428 SDHB|NM_003000_exon_2_0_chr1_17350468_r_0_2563051 1000 +
chr1 17350619 17350669 SDHB|NM_003000_exon_2_0_chr1_17350468_r_0_2563051 1000 -
chr1 17354413 17354463 SDHB|NM_003000_exon_3_0_chr1_17354244_r_0_2563052 1000 -
chr1 17354152 17354202 SDHB|NM_003000_exon_3_0_chr1_17354244_r_0_2563052 1000 +

"target_cancer_panel_2.0.bed" file used as Target file, contents(first 10 lines) as follows :

chr1 1981908 1982140 PRKCZ|NM_002744_exon_0_0_chr1_1981909_f
chr1 1986879 1987001 PRKCZ|NM_002744_exon_1_0_chr1_1986880_f
chr1 1987922 1988012 PRKCZ|NM_002744_exon_2_0_chr1_1987923_f
chr1 1990979 1991030 PRKCZ|NM_002744_exon_3_0_chr1_1990980_f
chr1 2005085 2005368 PRKCZ|NM_001033581_exon_0_0_chr1_2005086_f
chr1 2005424 2005714 PRKCZ|NM_001242874_exon_0_0_chr1_2005425_f
chr1 2036154 2036334 PRKCZ|NM_001033582_exon_0_0_chr1_2036155_f
chr1 2066700 2066786 PRKCZ|NM_001033581_exon_1_0_chr1_2066701_f
chr1 2075648 2075780 PRKCZ|NM_001033581_exon_2_0_chr1_2075649_f
chr1 2077465 2077547 PRKCZ|NM_001033581_exon_3_0_chr1_2077466_f

Please let me understand what kind of header it requires.

Answers

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