getting the same message as --help every time

[bbista]

Hello,

I keep getting this message every time I try to run this:

                   _ _      _   __           _

_ __ __ _ _ __ __ | | | | | / / __ _ | | ____
| ' \ / | '__/ _ | | |/ _ \ |/ / / ` / __| _| /
| |) | (| | | | (| | | | / / /| (| _ \ | / /
| .__/ _,|| _,|||_|_/_,|/_/|v0.1
||
parallelLastz: Run lastz jobs in parallel
Contact: jnarayan81@gmail.com for support

parallelLastz 0.1

Usage: /work/GGA_circos/maskedgenome/parallelLastz/parallelLastz.pl --qfile <> --tfile <> --cfile <> --speedup <#>

Options:
--qfile|-q query multifasta/fasta file
--tfile|-t target genome file
--cfile|-c config file
--speedup|-s number of core to use
--length|-l length below this is ignored
--unmask|-u unmask the lowercase in t and q file
--wipe|-w wipe out the intermediate files
--help|-h brief help message

The command I am using is:

perl /work/GGA_circos/maskedgenome/parallelLastz/parallelLastz.pl -q /work/GGA_circos/maskedgenome/parallelLastz/testDATA/qsample1.fa -t /work/GGA_circos/maskedgenome/parallelLastz/testDATA/tsample.fa -c /work/GGA_circos/maskedgenome/parallelLastz/conf --speedup 36

I am not sure what is wrong.

Any help is greatly appreciated.

Best,
Basanta

[jnarayan81]

Hi @bbista
Thanks for the update. There appears to be an issue with flags. I will fix it...

Try this:
perl parallelLastz.pl -q testDATA/qsample1.fa -t testDATA/tsample.fa -c conf -s 4 -w -l 10