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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
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reduce reads error

matan8matan8 Member
edited August 2012 in Ask the GATK team

Hi all,
I am trying to use the new feature "reduceReads" and I get an error everytime.
Can anyone tell me what is the problem?
BTW, I am working on yeast's genome and not human, if it is matter.

INFO 14:21:07,687 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:21:07,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.0-36-gf5c1c1a, Compiled 2012/08/08 20:17:07
INFO 14:21:07,688 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:21:07,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 14:21:07,689 HelpFormatter - Program Args: -R /home/mps/references/SK1_v2/fasta/SK1_v2.fixed.fa -T ReduceReads -I output.marked.realigned.fixed.recal.bam -o output.marked.realigned.fixed.recal.reduced.bam -l INFO
INFO 14:21:07,689 HelpFormatter - Date/Time: 2012/08/09 14:21:07
INFO 14:21:07,689 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:21:07,690 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:21:07,759 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:21:07,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 14:21:07,804 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 14:21:08,076 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 14:21:08,076 TraversalEngine - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 14:21:38,548 TraversalEngine - SK1.chr01:63354 3.90e+04 30.5 s 13.0 m 0.5% 98.2 m 97.7 m
INFO 14:22:08,706 TraversalEngine - SK1.chr01:79167 5.20e+04 60.6 s 19.4 m 0.6% 2.6 h 2.6 h
INFO 14:22:38,976 TraversalEngine - SK1.chr01:98653 6.90e+04 90.9 s 22.0 m 0.8% 3.1 h 3.1 h
INFO 14:23:10,903 TraversalEngine - SK1.chr01:114413 8.20e+04 2.0 m 25.0 m 0.9% 3.7 h 3.6 h
INFO 14:23:43,523 TraversalEngine - SK1.chr01:125477 9.20e+04 2.6 m 28.2 m 1.0% 4.2 h 4.2 h
INFO 14:24:15,215 TraversalEngine - SK1.chr01:145667 1.09e+05 3.1 m 28.6 m 1.2% 4.4 h 4.3 h
INFO 14:24:45,785 TraversalEngine - SK1.chr01:163339 1.23e+05 3.6 m 29.5 m 1.3% 4.5 h 4.5 h
INFO 14:25:17,660 TraversalEngine - SK1.chr01:179555 1.46e+05 4.2 m 28.5 m 1.5% 4.7 h 4.7 h
INFO 14:25:49,088 TraversalEngine - SK1.chr01:213605 1.71e+05 4.7 m 27.4 m 1.7% 4.5 h 4.4 h
INFO 14:25:51,716 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArithmeticException: / by zero
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.downsampleVariantRegion(SlidingWindow.java:539)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:498)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:520)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.close(SlidingWindow.java:562)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.addAlignment(SingleSampleCompressor.java:64)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:70)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:344)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:83)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:107)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:52)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:71)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.0-36-gf5c1c1a):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: / by zero
ERROR ------------------------------------------------------------------------------------------
Tagged:

Answers

  • CarneiroCarneiro Charlestown, MAMember

    I am working on this bug right now, but if you want it to work, simply turn the downsampler off with the option -ds 0. I'll update this thread as soon as I fix the downsampler.

  • CarneiroCarneiro Charlestown, MAMember

    Nevermind, I just fixed it and pushed. As soon as the new release comes up you can download it and it will work (it takes a couple hours to pass all internal tests before it gets automatically released and posted to the website)

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