The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Error with ClipReads

PrindleMPrindleM University of WashingtonMember Posts: 1

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
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 - 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

at java.util.TimSort.countRunAndMakeAscending(
at java.util.TimSort.sort(
at java.util.Arrays.sort(
at net.sf.samtools.util.SortingCollection$InMemoryIterator.(
at net.sf.samtools.util.SortingCollection.iterator(
at net.sf.samtools.util.SortingCollection.iterator(
at net.sf.samtools.SAMFileWriterImpl.close(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-4-g6f46d11):
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
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------


Sign In or Register to comment.