Tagged with #base recalibrator
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Hi,

I was running GATK BaseRecalibrator and came across "Stack Trace" error after completion of 58.6% . I ran the same command before with another bam file and it ran fine. Both of the bam files were produced using BWA MEM, sorted, indexed, fixed mate information (samtools) and then duplicate removed by PICARD.

My command is as follows:

java -Xmx4g -jar GenomeAnalysisTK.jar \

-T BaseRecalibrator \ -I "$sampleID".GATK.realigned.bam \ -R $humanRefSequence \ -knownSites $humanDbsnpFile \ -o "$sampleID".recal_data.grp

And the output are as follows:

INFO 16:22:06,245 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:22:06,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36 INFO 16:22:06,248 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:22:06,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:22:06,252 HelpFormatter - Program Args: -T BaseRecalibrator -I SK-PHP-pool2_S2.GATK.realigned.bam -R /scratch/fr1u11/ACE/REF_GENOME/HG19/b37_karyotypicallySorted/human_g1k_v37.fasta -knownSites /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf -o SK-PHP-pool2_S2.recal_data.grp INFO 16:22:06,252 HelpFormatter - Date/Time: 2013/04/25 16:22:06 INFO 16:22:06,252 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:22:06,252 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:22:06,317 ArgumentTypeDescriptor - Dynamically determined type of /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf to be VCF INFO 16:22:06,914 GenomeAnalysisEngine - Strictness is SILENT INFO 16:22:07,028 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 16:22:07,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 16:22:07,072 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 INFO 16:22:07,109 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf INFO 16:22:07,549 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files INFO 16:22:07,554 GenomeAnalysisEngine - Done creating shard strategy INFO 16:22:07,555 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 16:22:07,555 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 16:22:07,576 BaseRecalibrator - The covariates being used here: INFO 16:22:07,576 BaseRecalibrator - ReadGroupCovariate INFO 16:22:07,576 BaseRecalibrator - QualityScoreCovariate INFO 16:22:07,576 BaseRecalibrator - ContextCovariate INFO 16:22:07,576 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 16:22:07,576 BaseRecalibrator - CycleCovariate INFO 16:22:07,596 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 16:22:07,596 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 16:22:37,574 ProgressMeter - 1:27547695 0.00e+00 30.0 s 49.6 w 0.9% 56.3 m 55.8 m INFO 16:23:07,584 ProgressMeter - 1:62606707 1.00e+05 60.0 s 10.0 m 2.0% 49.5 m 48.5 m INFO 16:23:37,594 ProgressMeter - 1:119405961 1.00e+05 90.0 s 15.0 m 3.8% 39.0 m 37.5 m INFO 16:24:07,605 ProgressMeter - 1:203302345 2.00e+05 120.0 s 10.0 m 6.6% 30.5 m 28.5 m INFO 16:24:37,616 ProgressMeter - 1:249191380 3.00e+05 2.5 m 8.3 m 8.0% 31.1 m 28.6 m INFO 16:25:08,493 ProgressMeter - 2:46544672 3.63e+05 3.0 m 8.3 m 9.5% 31.5 m 28.5 m INFO 16:25:38,503 ProgressMeter - 2:97745730 4.63e+05 3.5 m 7.6 m 11.2% 31.3 m 27.8 m INFO 16:26:08,517 ProgressMeter - 2:141375959 5.63e+05 4.0 m 7.1 m 12.6% 31.8 m 27.8 m INFO 16:26:38,527 ProgressMeter - 2:221046892 5.63e+05 4.5 m 8.0 m 15.2% 29.7 m 25.2 m INFO 16:27:08,538 ProgressMeter - 3:10071132 6.99e+05 5.0 m 7.2 m 16.2% 30.9 m 25.9 m INFO 16:27:38,548 ProgressMeter - 3:66821801 6.99e+05 5.5 m 7.9 m 18.0% 30.5 m 25.0 m INFO 16:28:08,559 ProgressMeter - 3:134762061 7.99e+05 6.0 m 7.5 m 20.2% 29.8 m 23.7 m INFO 16:28:38,842 ProgressMeter - 3:191481932 8.99e+05 6.5 m 7.3 m 22.0% 29.6 m 23.0 m INFO 16:29:08,853 ProgressMeter - 4:34101052 9.64e+05 7.0 m 7.3 m 23.4% 30.0 m 23.0 m INFO 16:29:38,863 ProgressMeter - 4:82832343 1.06e+06 7.5 m 7.1 m 24.9% 30.2 m 22.6 m INFO 16:30:08,874 ProgressMeter - 4:151647250 1.06e+06 8.0 m 7.5 m 27.1% 29.5 m 21.5 m INFO 16:30:38,884 ProgressMeter - 5:3806120 1.21e+06 8.5 m 7.0 m 28.5% 29.8 m 21.3 m INFO 16:31:08,895 ProgressMeter - 5:79596315 1.21e+06 9.0 m 7.4 m 31.0% 29.1 m 20.1 m INFO 16:31:38,905 ProgressMeter - 5:143680795 1.31e+06 9.5 m 7.3 m 33.1% 28.8 m 19.3 m INFO 16:32:08,916 ProgressMeter - 5:180678089 1.41e+06 10.0 m 7.1 m 34.2% 29.2 m 19.2 m INFO 16:32:38,926 ProgressMeter - 6:58717151 1.45e+06 10.5 m 7.3 m 36.1% 29.1 m 18.6 m INFO 16:33:08,937 ProgressMeter - 6:117106171 1.55e+06 11.0 m 7.1 m 38.0% 29.0 m 18.0 m INFO 16:33:38,947 ProgressMeter - 6:170991744 1.65e+06 11.5 m 7.0 m 39.8% 29.0 m 17.4 m INFO 16:34:08,958 ProgressMeter - 7:50243192 1.68e+06 12.0 m 7.1 m 41.4% 29.0 m 17.0 m INFO 16:34:38,968 ProgressMeter - 7:101200087 1.78e+06 12.5 m 7.0 m 43.0% 29.1 m 16.6 m INFO 16:35:08,979 ProgressMeter - 7:156036181 1.88e+06 13.0 m 6.9 m 44.8% 29.1 m 16.0 m INFO 16:35:38,988 ProgressMeter - 8:37364205 1.93e+06 13.5 m 7.0 m 46.1% 29.3 m 15.8 m INFO 16:36:08,998 ProgressMeter - 8:97079882 2.03e+06 14.0 m 6.9 m 48.0% 29.2 m 15.2 m INFO 16:36:39,008 ProgressMeter - 8:146292633 2.13e+06 14.5 m 6.8 m 49.6% 29.3 m 14.7 m INFO 16:37:09,018 ProgressMeter - 9:89065984 2.13e+06 15.0 m 7.1 m 52.5% 28.6 m 13.6 m INFO 16:37:39,028 ProgressMeter - 9:135394782 2.23e+06 15.5 m 7.0 m 54.0% 28.7 m 13.2 m INFO 16:38:09,038 ProgressMeter - 10:30154466 2.30e+06 16.0 m 7.0 m 55.1% 29.0 m 13.0 m INFO 16:38:39,048 ProgressMeter - 10:86113015 2.40e+06 16.5 m 6.9 m 57.0% 29.0 m 12.5 m INFO 16:39:09,058 ProgressMeter - 11:1747804 2.51e+06 17.0 m 6.8 m 58.6% 29.0 m 12.0 m INFO 16:39:39,069 ProgressMeter - 11:1877044 2.61e+06 17.5 m 6.7 m 58.6% 29.9 m 12.4 m INFO 16:40:09,079 ProgressMeter - 11:2008155 2.71e+06 18.0 m 6.7 m 58.6% 30.7 m 12.7 m INFO 16:40:39,090 ProgressMeter - 11:2124930 2.81e+06 18.5 m 6.6 m 58.6% 31.6 m 13.1 m INFO 16:41:09,101 ProgressMeter - 11:2259894 2.91e+06 19.0 m 6.5 m 58.6% 32.4 m 13.4 m INFO 16:41:39,112 ProgressMeter - 11:2389552 3.01e+06 19.5 m 6.5 m 58.6% 33.3 m 13.8 m INFO 16:42:09,122 ProgressMeter - 11:2530316 3.11e+06 20.0 m 6.4 m 58.6% 34.1 m 14.1 m INFO 16:42:39,133 ProgressMeter - 11:2647149 3.21e+06 20.5 m 6.4 m 58.6% 35.0 m 14.5 m INFO 16:43:09,143 ProgressMeter - 11:2764819 3.31e+06 21.0 m 6.4 m 58.6% 35.8 m 14.8 m INFO 16:43:39,154 ProgressMeter - 11:2889029 3.41e+06 21.5 m 6.3 m 58.6% 36.7 m 15.2 m INFO 16:44:04,517 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: 251 at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsIndel(BaseRecalibrator.java:387) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253) 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.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:109) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283) 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 2.4-9-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: 251
ERROR ------------------------------------------------------------------------------------------

It would be most helpful if someone can tell me what might be reason causing the problem. Many thanks in advance.

Regards