Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.

The following error message after I run the command:java -jar /home/zhangjing/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T SplitNCigarReads -R /media/chao/Piapia/home/chao/Documents/BFC2013031/pig102.fa -I PBS_SRR1047797.dedup_reads.bam -o PBS_SRR1047797.dedup_reads.splitN.bam -U ALLOW_N_CIGAR_READS

INFO 09:32:31,632 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 09:32:31,687 ReadShardBalancer$1 - Loading BAM index data
INFO 09:32:31,688 ReadShardBalancer$1 - Done loading BAM index data
INFO 09:33:01,635 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: SAM/BAM/CRAM file [email protected]e941cc8 appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 71; please see the GATK --help documentation for options related to this error
ERROR -----------------------------------------------------------------------------------------

I wonder what‘s wrong with my inputfile or command line??


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