Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp -Xmx7g -Xms256m
[Wed Apr 22 22:21:55 CDT 2020] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp/tmp-gatk-FCsWXU/gatk_input.fasta OUTPUT=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp/tmp-gatk-FCsWXU/dict7481932586338388707.tmp    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Apr 22 22:22:04 CDT 2020] Executing as g2main@roundup64 on Linux 3.10.0-1062.18.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057)
[Wed Apr 22 22:22:09 CDT 2020] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=750256128
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported): 
##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Contig chr20 given as location, but this contig isn't present in the Fasta sequence dictionary
##### ERROR ------------------------------------------------------------------------------------------
mv: cannot stat ‘/galaxy-repl/main/files/039/619/dataset_39619384.dat.sample_summary’: No such file or directory