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Singnification of an Error to run unified genotyper

etricaenetricaen montpellier, FranceMember

hello,
i tried to launch unified genotyper but it's seems doesnt worked. i show you the error msg:

[[email protected] palmx_bam]$ /usr/local/java/latest/bin/java -jar /home/sabotf/sources/GenomeAnalysisTK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ./Eg_RNA_RefSeq_MyOPGP.fasta -nt \$NSLOTS -I ./merged_bams_file.bam -o ./merged_bams_file.vcf -stand_call_conf 30 -stand_emit_conf 10 -rf BadCigar

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Invalid command line: Failed to parse value [email protected]c12050 for argument numberOfDataThreads. This is most commonly caused by providing an incorrect data type (e.g. a double when an int is required)
ERROR ------------------------------------------------------------------------------------------

What does it means ?

Best Answer

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