CAP3 not giving consensus and singlet files as output

[Alirez]

Hi all,

I'm a bit confused as to why CAP3 is not giving .singlet and .contig output files as specified in the manual. The only output I am getting is the report of the assembly which I redirect from standard output.

There doesn't seem to be an option for toggling these outputs on/off. I have a script which can extract the consensus sequences from the report, but the .singlets file (with reads not incorporated into an assembly) is important.

Can anyone offer some help as to why I'm unable to generate these outputs?

Thanks.


ps. The command I am using is:

cap3 input.fa > output.report

[Alirez]

Problem solved...

In case anyone is interested, when cap3 is called from a python script (using os.system) all the desired output files are produced. I haven't tested this yet, but it may well work for bash and perl as well.

A