GATK RealignerTargetCreator error

binlangmanbinlangman 湖南长沙Member

Hello! I am working with some Illumina FASTQ files. I used bwa to align the data. I then sorted, indexed and marked the bam file for PCR duplicates using picard. And then in order to realign around the indels, I used the RealignerTargetCreator. Here is the error:

INFO 11:12:43,040 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:12:43,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51
INFO 11:12:43,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:12:43,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:12:43,048 HelpFormatter - Program Args: -T RealignerTargetCreator -R NC_010473.fasta -I dedup_reads.bam -o target_intervals.list
INFO 11:12:43,049 HelpFormatter - Date/Time: 2013/12/26 11:12:43
INFO 11:12:43,049 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:12:43,049 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:12:43,708 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:12:44,116 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:12:44,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:12:44,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 11:12:44,237 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:12:44,361 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:12:44,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:12:44,361 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 11:12:48,747 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: SAM/BAM file SAMFileReader{/home/lmbin/dedup_reads.bam} appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 63; please see the GATK --help documentation for options related to this error
ERROR ------------------------------------------------------------------------------------------

I'm a greener, I don't know how to solve the problem in order to finish realignment. Can you give some advice?

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