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The parameters of Module 'draft-path' #129
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Yes. The name of the daligner database as |
@govinda-kamath , |
Which commit of the software are you running? |
I install it in Jun 28,2017 with git clone. |
should give you the commit that you installed. But it's weird that there is no G3. |
The first few rows look like this: |
This should actually still be producing a |
464K Sep 12 14:29 hsy50x.G2c.graphml |
It looks like something went wrong in the Can you return the STDOUT of the run of the |
command: output: Files generated: 756K Sep 12 16:50 hsy50x.G2.graphml |
Can you give us the |
I can provide it to you. It must be a mistake of your program. And now I want to know, is it ok if I use G2 file? |
Sure. You can. Though it looks like the code crashed somewhere there (so I'm not sure about if the results will be kosher). |
it needs one or two day to get the file 'hsy.hinge.list'. |
Another question, do you think HINGE is suited for a large genome with relative high repeat content? The size of our genome is ~1 Gb. |
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'.
And I will mail it to you after I rerun the program. Can you provide me
your email?
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<#129 (comment)>,
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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 large genome with
relative high repeat content?
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~1 Gb |
Hinge should work for a 1 GB genome.
…On Tue, Sep 12, 2017 at 2:39 PM, Nott Yu ***@***.***> wrote:
~1 Gb
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Have you received my email? |
Yes. We'll get back to you soon. |
There were a few small issues with hinge clip that were preventing it from creating the G3 graph. We created a new branch called devG3, which should fix that. In order to have the G3 graph produced, you should make sure that
Let us know if this works. |
OK, I'll install devG3 branch and try as you suggested. I'll give you a reply as I get a result. |
Before I report my result I want to say another thing: Your tool is really difficult to compile. I'm serious. I will try to install the devG3 branch and try again. And I hope this error message can help you solve other problems of hinge. I'll report the progess of devG3 in this issue later. |
These are just reports on the graph about visualisation, not error messages. You should be able to continue on the pipeline. |
Dear developer,
I want to make sure some parameters that module 'draft-path' uses.
hinge draft-path $PWD $db hsy50x.G2.graphml
In your manual, you write G2. But in a issue,'#77', you write G3 there. Is there any difference?
thank you.
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