[maker-devel] Problem with installation

[Daniel Ence]

Hi Panos, The results are stored in the datastore directory in the "maker.output" directory. You can merge those results into one gff file with the gff3_merge accessory script. It's included in the bin directory.

~Daniel


Daniel Ence
Graduate Student
dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On May 29, 2014, at 3:21 AM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>>
 wrote:

So I managed to install it on my workstation and it works fine! Thanks for the information on perlbrew. I will also give it a try.

I did a test run on my workstation using just a few contigs and was wondering where the annotation is saved. Is it the gff files (one gff per contig) in the *.maker.output/ directory?




On Wed, May 28, 2014 at 6:28 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Try perlbrew to set up yor own local version of perl just for your user.
http://perlbrew.pl<http://perlbrew.pl/>

--Carson


From: Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>>
Date: Wednesday, May 28, 2014 at 10:13 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Daniel Ence <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>>, "<maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>

Subject: Re: [maker-devel] Problem with installation

Hello Daniel and Carson,

Thank you both for your comments.

Carson, I gave it a lot more than 30 seconds. I gave it about 5 minutes but still nothing happens.

Daniel, the same is true for maker -CTL; it appears as if it's doing something, but if you give a top you'll see that the CPU usage is ALWAYS 0%.

Three things that might be helpful:
1. Ctrl-C doesn't work for killing maker; you have to give "kill -9 <PID>"
2. when I give top I see that there are two maker processes running. Is this normal?
3. When I press Ctrl-C, the resources in top (labeled VIRT, RES and SHR - I guess that's memory) for one of the two maker processes go to zero, but it doesn't go away.





On Wed, May 28, 2014 at 4:32 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Perl is a scripting language rather than a compiled language, and one thing that happens when you first use a new module or script Is that the interpreter follows the dependency tree validating that everything executes/loads correctly.  Since you installed a number of dependencies and MAKER itself, the first time you launch MAKER Perl has to do this check on the dependency tree.  This only happens the first time, and after that Perl remembers it already ran the check so the dependencies and MAKER will just start from then on.  Normally this proccess takes less than 30 seconds; however, on some systems (especially clusters) there may a  heavy IO burden and this process can take a while.  For example does it take a moment for 'ls -al' to return in some directories rather than returning instantaneously like it is supposed to?  If it takes 3 seconds to return or example, then each dependency check may take up to 3 seconds.  If you just installed a bunch of new perl modules then there may be a hundred or more dependencies that may have to be validated for the first time.

--Carson



From: Daniel Ence <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>>
Date: Wednesday, May 28, 2014 at 7:29 AM
To: Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>>
Cc: "<maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Problem with installation

Hi Panos, When you go to the src directory and type "./Build status", what message do you get? Also, what version of maker are you running?

Thanks,
Daniel


Daniel Ence
Graduate Student
dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On May 28, 2014, at 1:28 AM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>>
 wrote:

Hello Maker community,

I just finished installing Maker and even though everything seems to be okay, when I give

./maker -h

or

./maker

the program apparently hangs without giving any output or warning or error.

Just so you know, I have installed all dependencies (Perl libraries and third-party programs) and am executing from bin/, not src/bin/.

Any ideas?

Panos
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