CAR parameters not work

Question

[Giffredo]

Hi, I used the CAR software http://www.ncbi.nlm.nih.gov/pubmed/25431302 in order to improve my prokaryotic genome assembly.

I download the CAR package and I use it. It works using:

php car.php ~/mydata/out.coords

but trying the - m parameters in the code (to obtain the fasta file as output), it doesn't work.

php car.php -m ~/mydata/out.coords

there is not a real error.. only return me this sentence: Usage: php car.php [option] <.coords file> [-r <reference.fna file="">, -q <draft.fna file="">] Using '-h' for help

I don't understand my error

Answer 1

[Sej Modha]

Did you try the following command instead of running the mummer separately?

 php car.php <-nuc/-pro> -m -r reference.fna -q contigs.fna

I have never used this program but it sounds like if you have run the nucmer/promer separately then the tool does not have access to the sequences, hence your command might work without option -m which is to output in multifasta format.

[Giffredo]

Thanks, you solved my problem.