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ERROR stack trace in ASEReadCounter

szimmermszimmerm Bronx, New YorkMember
edited June 2015 in Ask the GATK team

Hi,

I was running ASEReadCounter and came across a "stack trace" error after completion of 14.1%.

I am running the command like this:

java -jar ../GenomeAnalysisTK-3.4-0/GenomeAnalysisTK.jar -R /results2/indexes/genomes/mm9/fasta/mm9.fa -T ASEReadCounter -o filterReadCounts.chr13.58264978.txt -I dedupFolder/D4.indel.recal.dedup.reordered.bam -sites variants/gatk/D4.allBases.chr13.vcf -minDepth 20 --minMappingQuality 30 --minBaseQuality 20

The output is as follows:

INFO 13:27:40,125 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:27:40,130 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
INFO 13:27:40,130 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:27:40,131 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:27:40,136 HelpFormatter - Program Args: -R /results2/indexes/genomes/mm9/fasta/mm9.fa -T ASEReadCounter -o filterReadCounts.chr13.58264978.txt -I dedupFolder/D4.indel.recal.dedup.reordered.bam -sites variants/gatk/D4.allBases.chr13.vcf -minDepth 20 --minMappingQuality 30 --minBaseQuality 20 -U ALLOW_N_CIGAR_READS -rf BadCigar
INFO 13:27:40,143 HelpFormatter - Executing as [email protected] on Linux 2.6.18-371.12.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_09-b05.
INFO 13:27:40,144 HelpFormatter - Date/Time: 2015/06/29 13:27:40
INFO 13:27:40,145 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:27:40,145 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:27:40,937 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:27:41,075 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
INFO 13:27:41,091 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:27:41,186 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
INFO 13:27:41,474 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 13:27:42,051 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:27:42,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:27:42,053 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:27:42,054 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 13:28:12,062 ProgressMeter - chr10:61439995 7224296.0 30.0 s 4.0 s 2.3% 21.6 m 21.1 m
INFO 13:28:42,066 ProgressMeter - chr10:107123365 1.4729978E7 60.0 s 4.0 s 4.0% 24.8 m 23.8 m
INFO 13:29:12,078 ProgressMeter - chr11:29429929 2.1979505E7 90.0 s 4.0 s 6.0% 25.0 m 23.5 m
INFO 13:29:42,085 ProgressMeter - chr11:67787354 2.8914135E7 120.0 s 4.0 s 7.4% 26.8 m 24.8 m
INFO 13:30:12,090 ProgressMeter - chr11:88702416 3.4725261E7 2.5 m 4.0 s 8.2% 30.3 m 27.8 m
INFO 13:30:42,095 ProgressMeter - chr11:110188026 4.0515208E7 3.0 m 4.0 s 9.0% 33.2 m 30.2 m
INFO 13:31:12,100 ProgressMeter - chr12:44912778 4.8755304E7 3.5 m 4.0 s 11.2% 31.3 m 27.8 m
INFO 13:31:42,107 ProgressMeter - chr12:104866935 5.6805392E7 4.0 m 4.0 s 13.4% 29.8 m 25.8 m
INFO 13:32:12,113 ProgressMeter - chr12:121257414 5.9799881E7 4.5 m 4.0 s 14.1% 32.0 m 27.5 m

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

java.lang.ArrayIndexOutOfBoundsException: 0
at org.broadinstitute.gatk.tools.walkers.rnaseq.ASEReadCounter.map(ASEReadCounter.java:216)
at org.broadinstitute.gatk.tools.walkers.rnaseq.ASEReadCounter.map(ASEReadCounter.java:102)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
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: 0
ERROR ------------------------------------------------------------------------------------------

Is there any reason for this error, or is it just a bug? My overall goal is to get the filtered count of reads that support a given allele for an individual sample. DepthPerAlleleBySample gives unfiltered counts instead of filtered ones. If there is a way to get the filtered counts besides using ASEReadCounter that would also be great. Thanks!

Issue · Github
by Sheila

Issue Number
1094
State
open
Last Updated
Assignee
Array
Milestone
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