I am currently running the genotypes program of Stacks for the purpose of generating joinmap file primarily to ultimately create a linkage map:

sample script I did: $STACKS_DIR/genotypes -b 1 -P $IN_GEN -r 2 -t F2 -o joinmap -o rgtl -o onemap

But I get this error: ./genotypes.sh: line 7: =/home/mmeel/Documents/DOST_SCP1/Hscabra_lnkmp/subset_lnkmp/stacks_subset/denovo_raw.subset/stacks.M1: No such file or directory Error: Failed to parse command line: '2' is seen as a positional argument. Expected no positional arguments.

I checked the spelling of my directory for the input file, I see no error. I wonder what could be the error.

I also do not understand the "failed to parse command line:.."

Thanks in advance for the help.