my script :
java -jar ~/bin/gatk-3.2-2/GenomeAnalysisTK.jar -T SplitNCigarReads -R Gmax.fa -I NPB18L_mark.bam -o NPB18L_snc.bam -U ALLOW_N_CIGAR_READS -fixNDN
when i use -fixNDN, it will be:
java.lang.UnsupportedOperationException
at java.util.AbstractList.add(AbstractList.java:148)
at java.util.AbstractList.add(AbstractList.java:108)
at org.broadinstitute.gatk.tools.walkers.rnaseq.SplitNCigarReads.initialize(SplitNCigarReads.java:150)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
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)
but i don't use -fixNDN, it will be:
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
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: Bad input: Cannot split this read (might be an empty section between Ns, for example 1N1D1N): 94M407N1D1033N6M
how can i fix it???