The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
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.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

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
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 - 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(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.close(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.addAlignment(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.0-36-gf5c1c1a):
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
ERROR MESSAGE: / by zero
ERROR ------------------------------------------------------------------------------------------


  • 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)

Sign In or Register to comment.