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:
sung@SungUbuntu:~/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 sung@SungUbuntu 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)