dwgsim arguments not working (on mac)

[adamhfreedman]

i can get dwgsim to generate the help menu, and if i stick the command line arguments after the reference genome file and outfile.fq names, it runs fine but uses the default settings, ignoring the arguments.

the correct order, per the wiki is:

dwgsim [options] <in.ref.fa> <out.bwa.read1.fq> <out.bwa.read2.fq> <out.bfast.fq>

but when i do this, .e.g:
dwgsim -e 0.01 -E 0.01 -d 500 -s 50 -N 100000 -1 100 -2 100 -r 0.0010 -R 0.10 -X 0.3 -n 0 /Volumes/Storage/CanidGenomes_Project/CanFam3/canfam3.fa out.bwa.read1.fq out.bwa.read2.fq out.bfast.fq

i get the following error:

[dwgsim_core] fail to open file '0.01'. Abort!

basically, dwgsim is trying to read the first argument as the reference file name.

is there some sort of mac specific argument parsing problem here, and if so, a solution?

[nilshomer]

Please run the version from the latest git and post your results. The options have changed, so please adjust accordingly.

[adamhfreedman]

solved it, but error during make

Thanks Nils, it works now.

The only other thing is that there were errors during make:

make[2]: *** No rule to make target `dwgsim_eval.pl', needed by `all-am'. Stop.
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[nilshomer]

Thanks Nils, it works now.

The only other thing is that there were errors during make:

make[2]: *** No rule to make target `dwgsim_eval.pl', needed by `all-am'. Stop.
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Thanks for the report, fixed in a new commit.