Question: stacks denovo output directory can't be read in running genotypes program
0
gravatar for jav
2.6 years ago by
jav0
Philippines
jav0 wrote:

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.

ADD COMMENTlink written 2.6 years ago by jav0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 973 users visited in the last hour
_