[Samtools-help] picard EstimateLibraryComplexity ArrayIndexOutOfBoundsException

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I’m getting an ArrayIndexOutOfBoundsException with picard EstimateLibraryComplexity. This happens with some bam files but not others from the same run, all Illumina paired end 50+50 aligned with Novoalign.

Here’s a typical STDERR:

[Thu May 26 18:51:17 PDT 2011] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/data/storage-1-02/archive/kmsquire/GBM_SPORE/GBM_SPORE/stage-03-sample-processing/IOIS_4149_SID_5256_initial_surgery/3-markdup/IOIS_4149_SID_5256_initial_surgery.novoalign.MarkDup.bam] OUTPUT=/scratch1/tmp/hlee/post-rmdup_metrics/IOIS_4149_SID_5256_initial_surgery.novoalign.MarkDup.bam.picard_metrics.librarycomplexity READ_NAME_REGEX=[^_]+_[^_]+_[0-9]+_([0-9]+)_([0-9]+)_([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR=/scratch1/tmp/hlee/tmp VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000000    MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 CREATE_INDEX=false CREATE_MD5_FILE=false
INFO	2011-05-26 18:51:17	EstimateLibraryComplexity	Will store 7747078 read pairs in memory before sorting.
INFO	2011-05-26 18:52:23	EstimateLibraryComplexity	Read 1000000 records.

...

INFO	2011-05-26 20:32:08	EstimateLibraryComplexity	Read 111000000 records.
INFO	2011-05-26 20:32:27	EstimateLibraryComplexity	Read 112000000 records.
[Thu May 26 20:32:42 PDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done. Elapsed time: 101.42 minutes.
Runtime.totalMemory()=4265017344
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3
	at net.sf.picard.sam.EstimateLibraryComplexity.passesQualityCheck(EstimateLibraryComplexity.java:452)
	at net.sf.picard.sam.EstimateLibraryComplexity.doWork(EstimateLibraryComplexity.java:244)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
	at net.sf.picard.sam.EstimateLibraryComplexity.main(EstimateLibraryComplexity.java:197)

ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myo...@uc...
970.691.8299

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