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bpow
Posts: 5Member ✭
New gatk version... trying out ReduceReads again.
6 of 8 exomes I tried were processed by ReduceReads just fine, but two throw the exception Removed too many insertions, header is now negative! (at different genomic locations).
I did not find any mention of this error in the GATK forums, is this a known problem?
Command line: java -Xmx6g -jar GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T ReduceReads -o test.rr.bam -I rr-too-many-insertions.bam
java -v: java version "1.6.0_27" Java(TM) SE Runtime Environment (build 1.6.0_27-b07) Java HotSpot(TM) 64-Bit Server VM (build 20.2-b06, mixed mode)
Run log:
INFO 16:03:26,898 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:03:27,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-0-g9593e74, Compiled 2012/12/17 16:58:19
INFO 16:03:27,383 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:03:27,383 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:03:27,388 HelpFormatter - Program Args: -R human_g1k_v37.fasta -T ReduceReads -o test.rr.bam -I rr-too-many-insertions.bam
INFO 16:03:27,388 HelpFormatter - Date/Time: 2012/12/18 16:03:26
INFO 16:03:27,388 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:03:27,388 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:03:27,471 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:03:27,577 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 16:03:27,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:03:27,620 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 16:03:27,656 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:03:27,657 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 16:03:27,714 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO 16:03:27,717 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO 16:03:27,739 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO 16:03:28,739 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Removed too many insertions, header is now negative!
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.HeaderElement.removeInsertionToTheRight(HeaderElement.java:151)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.updateHeaderCounts(SlidingWindow.java:881)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.removeFromHeader(SlidingWindow.java:816)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:604)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:623)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:643)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:226)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:215)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:254)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-0-g9593e74):
##### 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: Removed too many insertions, header is now negative!
##### ERROR ------------------------------------------------------------------------------------------
(there is no progress listed here because this log is from after I bisected to find a narrow region where the problem is occuring).
Answers
Hmm, that's a new one. Could you please upload the slice of BAM where you're encountering the error?
Instructions here if needed: http://www.broadinstitute.org/gatk/guide/article?id=1894
Geraldine Van der Auwera, PhD
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0 • Off Topic Disagree Agree Like WTF •I uploaded a set of reads that gives the error in the archive
rr-too-many-insertions.tar.gzThanks.
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0 • Off Topic Disagree Agree Like WTF •Hi there,
Thank you very much for reporting this bug and providing a test file - it was extremely helpful! I just put together a fix that will be available in the next release (2.4).
Eric Banks, PhD -- Group Leader, Methods Development, MPG, Broad Institute of Harvard and MIT
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0 • Off Topic Disagree Agree Like WTF •Thanks for looking into this so promptly (and for putting the fix in a patch release instead of waiting for the next point version).
I've marked this as answered since I can now successfully run ReduceReads on my samples. Now I'm back to getting the "Somehow the requested coordinate is not covered by the read. Too many deletions?" error when I try the HaplotypeCaller. Since that's a separate issue, I'll address it its previous thread if I can't find anything wrong with my input files.
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0 • Off Topic Disagree Agree Like WTF •I'm using GATK 2.5-2-gf57256b. still have this error. shall i upload the bam file?
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •Hi Crocea, can you try the nightly build and see if it still happens ? we have pushed a recent fix on this issue that could resolve your problem.
Mauricio Carneiro, PhD http://www.broadinstitute.org/~carneiro/
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0 • Off Topic Disagree Agree Like WTF •ok. it's running and seems to be working. thanks
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •I have to retract what i said. this error is still there. with latest nightly. do you need the bam file?
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •Yes, please. Please see the instructions on how to upload test files. Thanks
Eric Banks, PhD -- Group Leader, Methods Development, MPG, Broad Institute of Harvard and MIT
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0 • Off Topic Disagree Agree Like WTF •Hi eric,
I uploaded the segment of the bam that caused the error. I followed this post , http://gatkforums.broadinstitute.org/discussion/1215/how-can-i-access-the-gsa-public-ftp-server#latest, and uploaded the file (132K) , "2317_645_vs_3280_by_2.Scaffold739.bam" to ftp://ftp.broadinstitute.org, the folder is "/ReduceReadsBug".
thanks, yu
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •Hi Yu,
Unfortunately we can't work with the data you provided. The post containing instructions for uploading test files is located here: http://gatkforums.broadinstitute.org/discussion/1894/how-do-i-submit-a-detailed-bug-report Thanks
Eric Banks, PhD -- Group Leader, Methods Development, MPG, Broad Institute of Harvard and MIT
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0 • Off Topic Disagree Agree Like WTF •OK. now i uploaded it with commandline, stack trace, fasta file (non-standard species, ), it's at ReduceReadsBug/ReduceReadsBug.tar.gz on ftp://ftp.broadinstitute.org.
thanks,
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •it's 835Mb due to the fasta file, still uploading.
Yu Huang http://www-scf.usc.edu/~yuhuang/
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0 • Off Topic Disagree Agree Like WTF •