Question: VelvetOptimiser getting an unknown option error
0
gravatar for Pryce Michener
2.3 years ago by
Memphis, TN
Pryce Michener10 wrote:

I'm trying to run VelvetOptimiser, and I keep getting the following error:

VelvetOptimiser.pl Version 2.2.5

Number of CPUs available: 32

Current free RAM: 122.174GB

Velvet OMP compiler setting: 1

Unknown option: fasta -shortpaired pairedreads_paired.fasta -fasta -short singlereads_singletons.fasta

This is my command:

perl ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl –s 51 –e 71 –o'-ins_length 350' -f '-fasta -shortPaired PairedReads_paired.fasta -fasta -short SingleReads_singletons.fasta'

Does anyone know what is happening here? For some reason it's getting rid of the "-" in front of fasta in the velveth options, but I can't seem to get it to work at all.

velvet assembly • 548 views
ADD COMMENTlink written 2.3 years ago by Pryce Michener10

Are you sure you have not copied and pasted the command from web or any other documents, as it sounds like a typical copy-paste command issue. Make sure that you type the entire command on the terminal and check if the error disappears!

ADD REPLYlink written 2.3 years ago by Sej Modha4.1k
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