Hi!

I am trying to run a single bam file with HaplotypeCaller tool of gatk4.2.3.0 version in order to get the corresponding g.vcf.gz file. 

My command looks as follows:

./gatk --java-options "-Xmx3g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" HaplotypeCaller \
-R /media/worky_ant/Seagate_Backup_Plus_Drive/AntropoGeoSNPs/reference/hs37d5.fa \
-I /media/worky_ant/Seagate_Backup_Plus_Drive/AntropoGeoSNPs/Jorge/HG00171.mapped.ILLUMINA.bwa.FIN.low_coverage.20120522.bam \
-O /media/worky_ant/Seagate_8T/Alicia_run/HG00171.g.vcf.gz

and I got this error:

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ', }' but no positional argument is defined for this tool.

***********************************************************************
org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional arguments were provided ', }' but no positional argument is defined for this tool.
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.propagateParsedValues(CommandLineArgumentParser.java:507)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:170)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:233)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:207)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
run_bam2vcf_GATK.sh: line 13: -I: command not found
run_bam2vcf_GATK.sh: line 14: -O: command not found

Could you please help me with this? 

Thanks!!