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Created 2013-12-17 10:21:02 | Updated | Tags: haplotypecaller runtime checkpoint
Comments (4)

I am using GATK 2.7 HC with Berkeley Lab Checkpoint/Restart (BLCR). After I checkpoint and restart my job on the cluster I get the stdout and stderr shown below. I think I got it, because the restart happened after midnight. Usually I just get incorrect estimates on total remaining runtime. Would it be possible to make GATK fully compatible with the use of BLCR? Thank you.

stdout: INFO 01:15:01,258 ProgressMeter - 1:28001706 0.00e+00 -4690921.0 s -9223372036.0 s 80.0% -5862401.0 s -1171480.0 s

stderr:

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

java.lang.IllegalArgumentException: runtime must be >= 0 but got -4690951902384272 at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.exceedsRuntimeLimit(GenomeAnalysisEngine.java:1200) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:329) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: runtime must be >= 0 but got -4690951902384272
ERROR ------------------------------------------------------------------------------------------

Created 2013-12-16 03:50:14 | Updated 2013-12-16 03:57:51 | Tags: haplotypecaller exception
Comments (4)

Hello,

This is in regards to a small exome capture experiment that I'd recently talked about here: http://gatkforums.broadinstitute.org/discussion/3531/bam-index-files-from-1000g-not-recognized-other-questions#latest . There are 8 experimental BAMs and 22 BAMs from 1000G supplied as inputs to HaplotypeCaller. And it quits with a code exception error at 52.1%. I've attached the relevant output. Also attached is the input files list. My OS info is:

Linux 3.2.0-56-generic #86-Ubuntu SMP x86_64 GNU/Linux

Any help would be greatly appreciated!

Thank you, Firas


Created 2013-09-04 19:24:19 | Updated | Tags:
Comments (26)

I am getting the following error while trying to recalibrate base quality scores at the AnalyzeCovariates step:

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

org.broadinstitute.sting.utils.R.RScriptExecutorException: RScript exited with 1. Run with -l DEBUG for more info. at org.broadinstitute.sting.utils.R.RScriptExecutor.exec(RScriptExecutor.java:174) at org.broadinstitute.sting.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:550) at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:380) at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:394) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.6-5-gba531bd):
ERROR
ERROR Please check the documentation guide 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: RScript exited with 1. Run with -l DEBUG for more info.
ERROR ------------------------------------------------------------------------------------------

Thanks, Katie


Created 2013-06-21 05:44:50 | Updated | Tags: haplotypecaller exception
Comments (8)

When trying to run the HaplotypeCaller in 2.6.2 with -nct I'm getting a number of crashes. Is NCT currently supported or is this experimental for the HaplotypeCaller currently? With the Multithreading I'm not exactly sure where the error is occurring and it's a pretty big bam. If needed I can try to narrow it down a bit further and create a subset bam...


../jre1.7.0_25/bin/java -jar ../GenomeAnalysisTK-2.6-2-ge03a5e9/GenomeAnalysisTK.jar -R ../refs/bosTau6.lic.fa -T HaplotypeCaller -I ../Chr15.ir.bam -bamout Chr15.bam -o Chr15.vcf.gz -L Chr15 -nct 5 -rf BadCigar

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NullPointerException
        at net.sf.samtools.SAMRecordCoordinateComparator.fileOrderCompare(SAMRecordCoordinateComparator.java:82)
        at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:43)
        at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:41)
        at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
        at java.util.TimSort.sort(Unknown Source)
        at java.util.Arrays.sort(Unknown Source)
        at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:203)
        at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
        at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
        at org.broadinstitute.sting.gatk.io.storage.SAMFileWriterStorage.addAlignment(SAMFileWriterStorage.java:94)
        at org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub.addAlignment(SAMFileWriterStub.java:307)
        at org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter.writeHaplotype(HaplotypeBAMWriter.java:310)
        at org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter.writeHaplotypesAsReads(HaplotypeBAMWriter.java:285)
        at org.broadinstitute.sting.utils.haplotypeBAMWriter.CalledHaplotypeBAMWriter.writeReadsAlignedToHaplotypes(CalledHaplotypeBAMWriter.java:87)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:733)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:138)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.6-2-ge03a5e9):
##### ERROR
##### ERROR Please check the documentation guide 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: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

and with more threads allowed:


../jre1.7.0_25/bin/java -jar ../GenomeAnalysisTK-2.6-2-ge03a5e9/GenomeAnalysisTK.jar -R ../refs/bosTau6.lic.fa -T HaplotypeCaller -I ../Chr15.ir.bam -bamout Chr15.bam -o Chr15.vcf.gz -L Chr15 -nct 16 -rf BadCigar

#### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.IllegalArgumentException: Comparison method violates its general contract!
        at java.util.TimSort.mergeLo(Unknown Source)
        at java.util.TimSort.mergeAt(Unknown Source)
        at java.util.TimSort.mergeCollapse(Unknown Source)
        at java.util.TimSort.sort(Unknown Source)
        at java.util.Arrays.sort(Unknown Source)
        at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:203)
        at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
        at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
        at org.broadinstitute.sting.gatk.io.storage.SAMFileWriterStorage.addAlignment(SAMFileWriterStorage.java:94)
        at org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub.addAlignment(SAMFileWriterStub.java:307)
        at org.broadinstitute.sting.utils.haplotypeBAMWriter.HaplotypeBAMWriter.writeReadAgainstHaplotype(HaplotypeBAMWriter.java:196)
        at org.broadinstitute.sting.utils.haplotypeBAMWriter.CalledHaplotypeBAMWriter.writeReadsAlignedToHaplotypes(CalledHaplotypeBAMWriter.java:103)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:733)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:138)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.6-2-ge03a5e9):
##### ERROR
##### ERROR Please check the documentation guide 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: Comparison method violates its general contract!
##### ERROR ------------------------------------------------------------------------------------------


Created 2013-05-23 00:23:30 | Updated | Tags: unifiedgenotyper reducereads
Comments (1)

I am using UnifiedGenotyper to call SNPs in certain regions from custom capture data. I previously had the pipeline working, but now I am trying with files that have been reduced using ReduceReads, and also changed to a newer version. I have many bam files, but I also get the error when I try with just two. See below for my script and the error message.

Many thanks.

java -Xmx20g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper \ -R human_g1k_v37.fasta \ -B:dbsnp,vcf dbsnp_132.b37.vcf \ -L baitgroupfile.picard \ -I file1.reduced.bam \ -I file2.reduced.bam \ -o out.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -G Standard \ -metrics out.metrics

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

net.sf.samtools.SAMFormatException: Unrecognized tag type: B at net.sf.samtools.BinaryTagCodec.readValue(BinaryTagCodec.java:270) at net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:220) at net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:302) at net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:282) at net.sf.samtools.SAMRecord.getAttribute(SAMRecord.java:830) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:132) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:803) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:769) at org.broadinstitute.sting.gatk.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:77) at org.broadinstitute.sting.gatk.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:19) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.(CountingFilteringIterator.java:59) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.applyDecoratingIterators(SAMDataSource.java:598) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.getIterator(SAMDataSource.java:517) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.seek(SAMDataSource.java:462) at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(MicroScheduler.java:150) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:56) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:209) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:109) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4905):
ERROR
ERROR Please visit to 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Unrecognized tag type: B
ERROR ------------------------------------------------------------------------------------------

Created 2013-03-26 20:46:26 | Updated 2013-03-27 16:21:14 | Tags: baserecalibrator error start stop
Comments (30)

Hello,

sorry if i missed the same problem in other threads in the forum... but we are having trouble running BaseRecalibrator in a sample and i couldn't find the solution.

I tried many steps and here is what i've found until now:

1 - Other samples work fine

2 - Running picard ValidateSamFile in realigned.bam (after IndelRealigner) gives many erros :
2a - Mate negative strand flag does not match read negative strand flag of mate
2b - Mate alignment does not match alignment start of mate
3c - Value was put into PairInfoMap more than once. (fatal)

3 - Running BaseRecalibrator with option -L 1:428-249250621 works fine!

After the fact that -L works fine i discarded the problem in vcf files and reference file. I don't know how to go further in this investigation since GATK 1 realined.bam also gives me the errors in (2) and those error are peanuts comparing the total number of reads.

The big difference here is that we're are using bwa7.

Any ideas? Thanks!

(i'm filtering out "secondary hits" given by bwa7 and will update this thread, if it works it may be helpful in the future)

GATK output:

INFO 14:11:47,441 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:11:47,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36 INFO 14:11:47,443 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:11:47,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 14:11:47,447 HelpFormatter - Program Args: -nct 8 -T BaseRecalibrator -I /mnt/work/rlb/pac661825//OUT_661825.realigned.bam -R ../data/databases//1KGP/GRCh37_female_exome_mt1kg.fasta --knownSites ../data/databases//dbSNP/dbSNP_137/00-All.vcf -o /mnt/work/rlb/pac661825//OUT_661825.grp INFO 14:11:47,447 HelpFormatter - Date/Time: 2013/03/26 14:11:47 INFO 14:11:47,447 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:11:47,447 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:11:47,458 ArgumentTypeDescriptor - Dynamically determined type of ../data/databases/dbSNP/dbSNP_137/00-All.vcf to be VCF INFO 14:11:47,500 GenomeAnalysisEngine - Strictness is SILENT INFO 14:11:47,558 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 14:11:47,565 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:11:47,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 14:11:47,587 RMDTrackBuilder - Loading Tribble index from disk for file ../data/databases/dbSNP/dbSNP_137/00-All.vcf INFO 14:11:47,704 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 8 processors available on this machine INFO 14:11:47,745 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files INFO 14:11:47,750 GenomeAnalysisEngine - Done creating shard strategy INFO 14:11:47,750 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 14:11:47,750 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 14:11:47,773 BaseRecalibrator - The covariates being used here:
INFO 14:11:47,773 BaseRecalibrator - ReadGroupCovariate INFO 14:11:47,773 BaseRecalibrator - QualityScoreCovariate INFO 14:11:47,773 BaseRecalibrator - ContextCovariate INFO 14:11:47,774 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 14:11:47,774 BaseRecalibrator - CycleCovariate INFO 14:11:47,776 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 14:11:47,777 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 14:12:18,626 ProgressMeter - 1:15956928 1.10e+06 30.0 s 28.0 s 0.5% 95.1 m 94.6 m INFO 14:12:48,655 ProgressMeter - 1:34102053 2.70e+06 60.0 s 22.0 s 1.1% 89.0 m 88.0 m INFO 14:13:18,685 ProgressMeter - 1:59096606 4.50e+06 90.0 s 20.0 s 1.9% 77.1 m 75.6 m INFO 14:13:48,714 ProgressMeter - 1:103467532 5.90e+06 120.0 s 20.0 s 3.4% 58.7 m 56.7 m INFO 14:14:18,745 ProgressMeter - 1:153234111 7.50e+06 2.5 m 20.0 s 5.0% 49.5 m 47.0 m INFO 14:14:48,774 ProgressMeter - 1:172414433 9.30e+06 3.0 m 19.0 s 5.7% 53.1 m 50.1 m INFO 14:15:19,054 ProgressMeter - 1:208266349 1.10e+07 3.5 m 19.0 s 6.9% 51.3 m 47.8 m INFO 14:15:49,095 ProgressMeter - 1:247611815 1.27e+07 4.0 m 19.0 s 8.2% 49.3 m 45.2 m INFO 14:15:56,507 GATKRunReport - Uploaded run statistics report to AWS S3

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (0) > (-1) STOP -- this should never happen -- call Mauricio! at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:537) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:176) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:389) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:392) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:244) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:679)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
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: START (0) > (-1) STOP -- this should never happen -- call Mauricio!
ERROR ------------------------------------------------------------------------------------------

Created 2013-02-11 21:52:27 | Updated 2013-02-11 22:08:09 | Tags: baserecalibrator
Comments (3)

Hi, I am trying to run the base recalibrator. For some of my sequences, it work perfectly, but for others, it's always crashing and giving the following error message :

INFO 16:49:21,718 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-6-gebbba25, Compiled 2013/01/08 19:29:18 INFO 16:49:21,720 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:49:21,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:49:21,724 HelpFormatter - Program Args: -T BaseRecalibrator -I alnSortedNoDupRGRealigned1.bam -l INFO -R 1.198.A.contig22.fa -knownSites alnSortedNoDupRGRealigned1_t0.01.vcf -o test.rcl -fixMisencodedQuals --filter_mismatching_base_and_quals INFO 16:49:21,725 HelpFormatter - Date/Time: 2013/02/11 16:49:21 INFO 16:49:21,725 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,725 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,737 ArgumentTypeDescriptor - Dynamically determined type of alnSortedNoDupRGRealigned1_t0.01.vcf to be VCF INFO 16:49:21,744 GenomeAnalysisEngine - Strictness is SILENT INFO 16:49:21,970 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 16:49:21,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 16:49:21,992 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 16:49:22,005 RMDTrackBuilder - Loading Tribble index from disk for file alnSortedNoDupRGRealigned1_t0.01.vcf INFO 16:49:22,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 16:49:22,040 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 16:49:22,134 BaseRecalibrator - The covariates being used here:
INFO 16:49:22,134 BaseRecalibrator - ReadGroupCovariate INFO 16:49:22,134 BaseRecalibrator - QualityScoreCovariate INFO 16:49:22,134 BaseRecalibrator - ContextCovariate INFO 16:49:22,135 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 16:49:22,135 BaseRecalibrator - CycleCovariate INFO 16:49:22,137 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3] INFO 16:49:22,138 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,139 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,139 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3] INFO 16:49:22,139 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3] INFO 16:49:22,140 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3] INFO 16:49:22,140 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,141 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,145 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 16:49:22,147 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 16:49:24,487 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: -31 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:225) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530) at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) 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:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):
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: -31
ERROR ------------------------------------------------------------------------------------------

Here is the command line I am using: java -Xmx4g -jar /mit/sjlabrie/software/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -I alnSortedNoDupRGRealigned1.bam \ -l INFO \ -R 1.198.A.contig22.fa \ -knownSites alnSortedNoDupRGRealigned1_t0.01.vcf \ -o test.rcl \ -fixMisencodedQuals \ --filter_mismatching_base_and_quals \

Any Idea what's going on ?

Thank you,

Simon


Created 2013-01-25 14:29:52 | Updated | Tags: error runtime
Comments (1)

INFO 17:40:38,765 ProgressMeter - chrX:147886444 3.21e+07 5.5 h 10.3 m 97.9% 5.6 h 7.1 m INFO 17:41:08,775 ProgressMeter - chrX:151653849 3.21e+07 5.5 h 10.3 m 98.0% 5.6 h 6.7 m INFO 17:41:38,785 ProgressMeter - chrX:153812787 3.22e+07 5.5 h 10.3 m 98.1% 5.6 h 6.5 m

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

java.lang.NoClassDefFoundError: net/sf/samtools/util/CloserUtil at net.sf.picard.util.PeekableIterator.close(PeekableIterator.java:46) at net.sf.picard.sam.MergingSamRecordIterator.addIfNotEmpty(MergingSamRecordIterator.java:169) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:125) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1091) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1057) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:24) at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:12) at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:36) at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:15) at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71) at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57) at org.broadinstitute.sting.gatk.datasources.reads.ReadShard.fill(ReadShard.java:135) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.advance(ReadShardBalancer.java:153) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:116) at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:75) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:65) 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:91) Caused by: java.lang.ClassNotFoundException: net.sf.samtools.util.CloserUtil at java.net.URLClassLoader$1.run(URLClassLoader.java:199) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:248) ... 29 more Caused by: java.util.zip.ZipException: error reading zip file at java.util.zip.ZipFile.read(Native Method) at java.util.zip.ZipFile.access$1200(ZipFile.java:29) at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:447) at java.util.zip.ZipFile$1.fill(ZipFile.java:230) at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141) at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:422) at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:358) at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:390) at java.util.jar.Attributes.read(Attributes.java:359) at java.util.jar.Manifest.read(Manifest.java:182) at java.util.jar.Manifest.(Manifest.java:52) at java.util.jar.JarFile.getManifestFromReference(JarFile.java:167) at java.util.jar.JarFile.getManifest(JarFile.java:148) at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:696) at java.net.URLClassLoader.defineClass(URLClassLoader.java:228) at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197) ... 34 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
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: net/sf/samtools/util/CloserUtil
ERROR ------------------------------------------------------------------------------------------

Any Idea what is the solution??


Created 2012-12-20 10:31:39 | Updated | Tags: unifiedgenotyper
Comments (7)

Hi,

I had a seemingly random RUNTIME ERROR previously (mentioned on this thread http://gatkforums.broadinstitute.org/discussion/1860/runtime-error-in-baserecalibrator-version-2-2-8-g99996f2), but I'm seeing this more and more for UnifiedGenotyper runs.

It seems that every 6-10 runs I get one or two that fail as below. Re-runinng seems to work correctly, but this is annoying to find that a 12hr job has died randomly. Please can this be investigated.

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

java.lang.NullPointerException at java.util.concurrent.locks.AbstractQueuedSynchronizer.hasQueuedPredecessors(AbstractQueuedSynchronizer.java:1453) at java.util.concurrent.locks.ReentrantLock$FairSync.tryAcquire(ReentrantLock.java:240) at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1136) at java.util.concurrent.locks.ReentrantLock$FairSync.lock(ReentrantLock.java:229) at java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:290) at java.util.concurrent.PriorityBlockingQueue.peek(PriorityBlockingQueue.java:286) at org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceNextValueInQueue(Reducer.java:89) at org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceAsMuchAsPossible(Reducer.java:120) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:510) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:636)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-8-g99996f2):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

My commandline is this: java -Xmx8g -jar GenomeAnalysisTKLite.jar -nct 4 -T UnifiedGenotyper --genotype_likelihoods_model BOTH --genotyping_mode DISCOVERY -R fastafile -I infile -o outfile --dbsnp dbsnp_137.b37.vcf -stand_call_conf 30 -stand_emit_conf 30

This usually coincides with errors is calling home code, although I don't know if it's cause or effect.

"INFO 16:41:33,533 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty INFO 16:41:33,534 HttpMethodDirector - Retrying request INFO 16:41:33,716 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty INFO 16:41:33,716 HttpMethodDirector - Retrying request INFO 16:41:33,897 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty INFO 16:41:33,897 HttpMethodDirector - Retrying request INFO 16:41:34,077 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty INFO 16:41:34,085 HttpMethodDirector - Retrying request INFO 16:41:34,267 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty INFO 16:41:34,267 HttpMethodDirector - Retrying request "