interval file for picard

Question

[bioguy24]

Appears not to like the interval files, but not sure why and no matter what I try I seem to get another error? Thanks.

Code:

dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools CalculateHsMetrics BI=sam_sort_index_5column_xgen_probes.bed TI=sam_sort_index_5column_xgen_targets.bed I=IonXpress_009_150603_newheader.bam  O=IonXpress_009_150603_all_IDT.CalculateHSmetrics
[Mon Jun 29 10:54:45 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=sam_sort_index_5column_xgen_probes.bed TARGET_INTERVALS=sam_sort_index_5column_xgen_targets.bed INPUT=IonXpress_009_150603_newheader.bam OUTPUT=IonXpress_009_150603_all_IDT.CalculateHSmetrics    TMP_DIR=/tmp/dnascopev VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Jun 29 10:54:45 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=61079552
Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 4 fields: chr1   133573  133692  -
    at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:192)
    at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152)
    at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83)
    at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
    at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)

Bait Intervals

@HD VN:1.4  GO:none SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr19    LN:59128983
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr22    LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrM LN:16569
chr1    133573  133692  -   chr1:133573-133692
chr1    659937  660056  -   chr1:659937-660056
chr1    809529  809649  +   chr1:809529-809649
chr1    955542  955662  +   chr1:955542-955662
chr1    955643  955763  +   chr1:955643-955763
chr1    957570  957690  +   chr1:957570-957690
chr1    957651  957771  +   chr1:957651-957771
chr1    957732  957852  +   chr1:957732-957852
chr1    970620  970740  +   chr1:970620-970740
chr1    976034  976154  +   chr1:976034-976154
chr1    976149  976269  +   chr1:976149-976269
chr1    976542  976662  +   chr1:976542-976662
chr1    976605  976725  +   chr1:976605-976725
chr1    976667  976787  +   chr1:976667-976787
chr1    976847  976967  +   chr1:976847-976967
chr1    976910  977030  +   chr1:976910-977030
chr1    976972  977092  +   chr1:976972-977092
chr1    977325  977445  +   chr1:977325-977445
chr1    977432  977552  +   chr1:977432-977552
chr1    978608  978728  +   chr1:978608-978728
chr1    978727  978847  +   chr1:978727-978847
chr1    978907  979027  +   chr1:978907-979027
chr1    979002  979122  +   chr1:979002-979122
chr1    979192  979312  +   chr1:979192-979312
chr1    979293  979413  +   chr1:979293-979413
chr1    979478  979598  +   chr1:979478-979598
chr1    979527  979647  +   chr1:979527-979647
chr1    979703  979823  +   chr1:979703-979823
chr1    979709  979829  +   chr1:979709-979829
chr1    980530  980650  +   chr1:980530-980650
chr1    980547  980667  +   chr1:980547-980667
chr1    980728  980848  +   chr1:980728-980848
chr1    980793  980913  +   chr1:980793-980913

Target Intervals

[Devon Ryan]

Ignore my (now deleted) reply :)

[Devon Ryan]

It looks like one of your files has entries spanning multiple lines. That would cause this problem.

[bioguy24]

Is it the BI= file?

chr1	980547	980667	+
	chr1:980547-980667
chr1	980728	980848	+
	chr1:980728-980848
chr1	980793	980913	+
	chr1:980793-980913

should be:

chr1	980547	980667	+     chr1:980547-980667
chr1	980728	980848	+     chr1:980728-980848
chr1	980793	980913	+     chr1:980793-980913

Thank you :).

[Devon Ryan]

Yup

[bioguy24]

All the intervals are on one line:

Now I am getting this error.

Exception in thread "main" net.sf.samtools.SAMFormatException: Unrecognized tag type: B

Thanks :)

[Devon Ryan]

What version of picard are you using?

[bioguy24]

Downloaded from

sudo apt-get install picard-tools

dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools --version
picard-tools
Copyright 2010 The Broad Institute

Thank you :)

[bioguy24]

Thank you for all your help, it is working now :)