Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp ERROR: Invalid argument ' '. USAGE: AddOrReplaceReadGroups [options] Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups Replace read groups in a BAM file.This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all reads to this read group in the OUTPUT BAM file. For more information about read groups, see the GATK Dictionary entry. (https://www.broadinstitute.org/gatk/guide/article?id=6472) This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH) (see http://ga4gh.org/#/documentation). Usage example: java -jar picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=output.bam \ RGID=4 \ RGLB=lib1 \ RGPL=illumina \ RGPU=unit1 \ RGSM=20 Version: 2.5.0-gradle-SNAPSHOT Options: --help -h Displays options specific to this tool. --stdhelp -H Displays options specific to this tool AND options common to all Picard command line tools. --version Displays program version. INPUT=String I=String Input file (BAM or SAM or a GA4GH url). Required. OUTPUT=File O=File Output file (BAM or SAM). Required. SORT_ORDER=SortOrder SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate} RGID=String ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default value. RGLB=String LB=String Read Group library Required. RGPL=String PL=String Read Group platform (e.g. illumina, solid) Required. RGPU=String PU=String Read Group platform unit (eg. run barcode) Required. RGSM=String SM=String Read Group sample name Required. RGCN=String CN=String Read Group sequencing center name Default value: null. RGDS=String DS=String Read Group description Default value: null. RGDT=Iso8601Date DT=Iso8601Date Read Group run date Default value: null. RGPI=Integer PI=Integer Read Group predicted insert size Default value: null. RGPG=String PG=String Read Group program group Default value: null. RGPM=String PM=String Read Group platform model Default value: null. /cromwell_root/exec.sh: line 8: : command not found /cromwell_root/exec.sh: line 9: : command not found /cromwell_root/exec.sh: line 10: #be: command not found /cromwell_root/exec.sh: line 11: library1: command not found /cromwell_root/exec.sh: line 12: : command not found /cromwell_root/exec.sh: line 13: : command not found /cromwell_root/exec.sh: line 14: : command not found /cromwell_root/exec.sh: line 15: : command not found