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error using ClipReads with commas for multiple cycles to clip

lucas careylucas carey Barcelona, SpainMember

Hi,
I want to remove cycles with high error rates. The following command works:
java -jar /homes/aplic/noarch/software/GATK/3.7-Java-1.8.0_74/GenomeAnalysisTK.jar -T ClipReads -R /gpfs42/projects/lab_lcarey/single_cell_behavior/Data/PhiX/NC_001422.fasta --clipRepresentation WRITE_NS_Q0S -I CRAM/180402_7001450_0415_ACC843ANXX__lane8_NoIndex_L008.cram -o CRAM_CLIPPED/180402_7001450_0415_ACC843ANXX__lane8_NoIndex_L008.bam -QT 30 -CT "1-2,3-4"
...
INFO 11:53:18,177 ClipReads - Creating Q-score clipper with threshold 30
INFO 11:53:18,177 ClipReads - Creating cycle clipper 0-1
INFO 11:53:18,178 ClipReads - Creating cycle clipper 2-3

but using a list with commas does not:
$ java -jar /homes/aplic/noarch/software/GATK/3.7-Java-1.8.0_74/GenomeAnalysisTK.jar -T ClipReads -R /gpfs42/projects/lab_lcarey/single_cell_behavior/Data/PhiX/NC_001422.fasta --clipRepresentation WRITE_NS_Q0S -I CRAM/180402_7001450_0415_ACC843ANXX__lane8_NoIndex_L008.cram -o CRAM_CLIPPED/180402_7001450_0415_ACC843ANXX__lane8_NoIndex_L008.bam -QT 30 -CT "1,2,3,4"
....
INFO 11:54:06,394 ClipReads - Creating Q-score clipper with threshold 30

ERROR --
ERROR stack trace

java.lang.RuntimeException: Badly formatted cyclesToClip argument: 1,2,3,4
at org.broadinstitute.gatk.tools.walkers.readutils.ClipReads.initialize(ClipReads.java:279)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Badly formatted cyclesToClip argument: 1,2,3,4
ERROR ------------------------------------------------------------------------------------------

Answers

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