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Error with ClipReads

PrindleMPrindleM University of WashingtonPosts: 1Member

I am trying to perform a -5 clip of bases at the beginning and end of my reads. Here is my command line and error stack. If it matters, I'm on a MacOS 10.7.5. I'd appreciate any help on what could have gone wrong.

$ java -jar -Xmx8g ~/Desktop/bioinformatics/DCS_1.22/programs/GenomeAnalysisTK.jar -T ClipReads -I seq_both_sscs_readgroups.bam -o seq_both_sscs_readgroups_clipped.bam -R /Users/mjpri/Desktop/bioinformatics/DCS_1.22/reference/human_g1k_v37.fasta --cyclesToTrim "1-5,71-75" --clipRepresentation HARDCLIP_BASES --fix_misencoded_quality_scores

INFO 13:02:48,642 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:02:48,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51 INFO 13:02:48,645 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:02:48,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:02:48,651 HelpFormatter - Program Args: -T ClipReads -I seq_both_sscs_readgroups.bam -o seq_both_sscs_readgroups_clipped.bam -R /Users/mjpri/Desktop/bioinformatics/DCS_1.22/reference/human_g1k_v37.fasta --cyclesToTrim 1-5,71-75 --clipRepresentation HARDCLIP_BASES --fix_misencoded_quality_scores INFO 13:02:48,651 HelpFormatter - Date/Time: 2013/10/31 13:02:48 INFO 13:02:48,651 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:02:48,652 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:02:49,828 GenomeAnalysisEngine - Strictness is SILENT INFO 13:02:50,012 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 13:02:50,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:02:50,042 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 13:02:50,137 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 13:02:50,143 GenomeAnalysisEngine - Done preparing for traversal INFO 13:02:50,143 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:02:50,143 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 13:02:50,145 ClipReads - Creating cycle clipper 0-4 INFO 13:02:50,146 ClipReads - Creating cycle clipper 70-74 INFO 13:02:50,147 ReadShardBalancer$1 - Loading BAM index data INFO 13:02:50,149 ReadShardBalancer$1 - Done loading BAM index data INFO 13:03:20,319 ProgressMeter - 19:50921238 3.09e+05 30.0 s 97.0 s 87.4% 34.0 s 4.0 s INFO 13:03:52,261 ProgressMeter - GL000192.1:73364 3.85e+05 61.0 s 2.7 m 100.0% 61.0 s 0.0 s INFO 13:04:31,643 ProgressMeter - GL000192.1:73364 3.85e+05 101.0 s 4.4 m 100.0% 101.0 s 0.0 s INFO 13:04:36,623 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.NullPointerException at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:51) at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:41) at java.util.TimSort.countRunAndMakeAscending(TimSort.java:329) at java.util.TimSort.sort(TimSort.java:203) at java.util.Arrays.sort(Arrays.java:727) at net.sf.samtools.util.SortingCollection$InMemoryIterator.(SortingCollection.java:335) at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:254) at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:43) at net.sf.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:190) at org.broadinstitute.sting.gatk.io.storage.SAMFileWriterStorage.close(SAMFileWriterStorage.java:99) at org.broadinstitute.sting.gatk.io.OutputTracker.close(OutputTracker.java:130) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:118) 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 2.7-4-g6f46d11):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
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