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Unknown Contig problem with SplitNCigarReads

sungjosungjo Member
edited August 2017 in Ask the GATK team

Hi everyone. I'm trying to run SplitNCigarReads on my STAR-aligned samples (using galaxy servers) that have gone through steps of Marking Duplicates & Sorting via Picard. Whenever I try to run SplitNCigarReads, it would run then stop at midpoint on Chromosome 1 and says that it's a bug of some sort.

It seems to be looking for unknown contig=chr1_KI270706v1_random

I am using Ubuntu 16.04.3 LTS, Java 1.8, latest GATK and picard. Latest ensemble reference FASTA file processed using this instruction: https://software.broadinstitute.org/gatk/documentation/article.php?id=1601

What can I do to get past this problem?

Error message is below:

[email protected]:~/Downloads$ java -jar /home/sung/Downloads/GATK.jar -R /home/sung/Downloads/reference.fa -T SplitNCigarReads -I /media/sung/ALIGNED/sample7ALL/7sorted_marked.bam -o /media/sung/ALIGNED/sample7ALL/7sorted_marked_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 17:13:48,677 HelpFormatter - ----------------------------------------------------------------------------------
INFO 17:13:48,680 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 17:13:48,681 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 17:13:48,681 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 17:13:48,681 HelpFormatter - [Fri Aug 18 17:13:48 CDT 2017] Executing on Linux 4.10.0-32-generic amd64
INFO 17:13:48,681 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01
INFO 17:13:48,684 HelpFormatter - Program Args: -R /home/sung/Downloads/reference.fa -T SplitNCigarReads -I /media/sung/ALIGNED/sample7ALL/7sorted_marked.bam -o /media/sung/ALIGNED/sample7ALL/7sorted_marked_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 17:13:48,695 HelpFormatter - Executing as [email protected] on Linux 4.10.0-32-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01.
INFO 17:13:48,695 HelpFormatter - Date/Time: 2017/08/18 17:13:48
INFO 17:13:48,696 HelpFormatter - ----------------------------------------------------------------------------------
INFO 17:13:48,696 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/sung/Downloads/GATK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 17:13:48,866 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 17:13:48,866 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 17:13:48,866 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:13:49,069 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 17:13:49,083 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:13:49,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.37
INFO 17:13:49,667 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 17:13:49,671 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:13:49,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:13:49,672 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:13:49,673 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 17:13:49,745 ReadShardBalancer$1 - Loading BAM index data
INFO 17:13:49,747 ReadShardBalancer$1 - Done loading BAM index data
INFO 17:14:19,855 ProgressMeter - chr1:8865289 700304.0 30.0 s 43.0 s 0.3% 3.0 h 3.0 h
INFO 17:14:49,856 ProgressMeter - chr1:21833897 1400554.0 60.0 s 42.0 s 0.7% 2.4 h 2.4 h
INFO 17:15:20,152 ProgressMeter - chr1:32228609 2300711.0 90.0 s 39.0 s 1.0% 2.5 h 2.5 h
INFO 17:15:51,892 ProgressMeter - chr1:43359997 3100783.0 2.0 m 39.0 s 1.4% 2.5 h 2.5 h
INFO 17:16:21,934 ProgressMeter - chr1:61088637 3900908.0 2.5 m 39.0 s 1.9% 2.2 h 2.2 h
INFO 17:16:53,919 ProgressMeter - chr1:94209347 4703175.0 3.1 m 39.0 s 2.9% 104.5 m 101.4 m
INFO 17:17:23,958 ProgressMeter - chr1:120452145 5603459.0 3.6 m 38.0 s 3.8% 95.0 m 91.5 m
INFO 17:17:53,959 ProgressMeter - chr1:153535998 6404745.0 4.1 m 38.0 s 4.8% 85.0 m 80.9 m
INFO 17:18:24,236 ProgressMeter - chr1:156338226 7105236.0 4.6 m 38.0 s 4.9% 93.7 m 89.2 m
INFO 17:18:56,154 ProgressMeter - chr1:180003227 7905261.0 5.1 m 38.0 s 5.6% 90.9 m 85.8 m
INFO 17:19:26,449 ProgressMeter - chr1:207337383 8605295.0 5.6 m 39.0 s 6.5% 86.7 m 81.1 m
INFO 17:19:58,263 ProgressMeter - chr1:228098773 9305345.0 6.1 m 39.0 s 7.1% 86.3 m 80.2 m

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: BUG: requested unknown contig=chr1_KI270706v1_random index=-1
at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.updateCache(MRUCachingSAMSequenceDictionary.java:178)
at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.getSequence(MRUCachingSAMSequenceDictionary.java:109)
at org.broadinstitute.gatk.utils.GenomeLocParser.validateGenomeLoc(GenomeLocParser.java:306)
at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:261)
at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:471)
at org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView.getReferenceContext(ReadReferenceView.java:98)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:140)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:128)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.aggregateMapData(TraverseReadsNano.java:119)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:101)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:107)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: BUG: requested unknown contig=chr1_KI270706v1_random index=-1
ERROR ------------------------------------------------------------------------------------------

Answers

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