Govinda Kamath

You should run ``` hinge maximal --db Stella --las Stella --mlas -x Stella --config /home/ag/HINGE/utils/nominal.ini hinge layout --db Stella --las Stella --mlas -x Stella --config /home/ag/HINGE/utils/nominal.ini -o Stella ``` The...

Yes. The name of the daligner database as `$db`. And you should use G2. `G3` is still an experimental module for larger genomes.

Which commit of the software are you running?

``` git log ``` should give you the commit that you installed. But it's weird that there is no G3.

This should actually still be producing a `G3` file. Can you confirm the size of the `G2` file?

It looks like something went wrong in the `clip` run. `G0`, `G1`, `G2`, `G3` are usually of similar sizes. Can you return the STDOUT of the run of the `draft-path`?

Can you give us the `hsy.edges.hinges` and `hsy.hinge.list` files? These files contain no sequence information, in case you're worried about privacy.

Sure. You can. Though it looks like the code crashed somewhere there (so I'm not sure about if the results will be kosher).

Please send it to [email protected] and [email protected]. On Tue, Sep 12, 2017 at 2:35 PM, Nott Yu wrote: > it needs one or two day to get the file 'hsy.hinge.list'....

How large a genome are you interested in? On Tue, Sep 12, 2017 at 2:36 PM, Nott Yu wrote: > Another question, do you think HINGE is suited for a...