[maker-devel] MAKER Install

[Barry Moore]

Hey Daniel,

We need to start running RepeatMasker with cross_match now that  
wublast is no longer available and ABBlast hasn't been released yet.   
Since we've always used wublast, I don't have an immediate answer to  
your question, but if cross_match is giving Seg Fault then you may  
need to send your error output to Phil Green (phg [ a t ]  
u.washington.edu).  You might also ask around your group and see if  
anyone has wublast installed so that you could use that for comparison.

B

On Sep 28, 2009, at 7:58 AM, Daniel Standage wrote:

> Barry's and Carson's suggestions were helpful, and SNAP is no longer  
> having any problems. However, solving the SNAP problem made some  
> other problems evident.  When I ran maker using the sample data,  
> there were some errors generated by RepeatMasker (see  
> maker_errors.log).  So I tried running RepeatMasker with some sample  
> data and got similar errors (see repeat_masker_*.log). I then looked  
> into all of RepeatMasker's prerequisites, and everything seems to be  
> working fine except for cross_match.  It ran for about 5 seconds  
> generating the output in cross_match_*.log, and then would have a  
> seg fault. I'm not really sure what the problem is or how to address  
> it.  Any suggestions?
>
> Thanks,
>
> Daniel Standage
> Plant Genetics Lab
> Brigham Young University
>
> On Tue, Sep 22, 2009 at 9:21 PM, Carson Holt <carson.holt at genetics.utah.edu 
> > wrote:
> Snap requires you to specify the location of the installation  
> directory, and will not automatically locate the HMM directory by  
> itself.  To do this you must set the environmental variable ZOE to  
> be the path to the snap installation directory.
>
> i.e. in you .bash_profile add something like the following.
>
> export ZOE=/usr/local/snap
>
> Please note that this is the location of the snap base directory and  
> not the Zoe or HMM directories under snap.
>
> You will then need to restart your terminal or type 'source  
> ~/.bash_profile' to finish loading all changes to your .bash_profile.
>
> When ZOE is not set, you must supply the full path to the HMM rather  
> than just the name, i.e. snaphmm:/usr/local/snap/HMM/fly
>
> Let me know if that fixes it for you.
>
> Thanks,
> Carson
>
> On Sep 22, 2009, at 5:21 PM, Daniel Standage wrote:
>
>> Hi all,
>>
>> I am trying to get Maker working on our system.  I finally have all  
>> of the prerequisites installed, and they all appear to be working  
>> fine.  I'm now using the example data to test maker and it is not  
>> working.  I created a directory for the test, copied over the test  
>> data, generated the control files, and made the following changes  
>> to the control files.
>> In maker_bopts.ctl
>> blast_type:ncbi
>> In maker_opts.ctl
>> genome:dpp_contig.fasta
>> est:dpp_transcripts.fasta
>> protein:dpp_proteins.fasta
>> snaphmm:fly
>> predictor:snap
>> Then when I run maker (using the command maker maker_exe.ctl  
>> maker_opts.ctl maker_bopts.ctl), it gives the following error  
>> message.
>>
>> #----------------------
>> FATAL: failed!!
>> #----------------------
>> ERROR: The snaphmm specified for Snap/Fathom in maker_opts.ctl does  
>> not exist.
>>
>> I verified that there is a "fly" file in SNAP's HMM directory, so I  
>> don't know what could be causing this.  Does anyone have any insight?
>>
>> Thanks,
>>
>> Daniel Standage
>> Plant Genetics Lab
>> Brigham Young University
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> < 
> cross_match_errors 
> .log 
> > 
> < 
> cross_match_output 
> .log 
> > 
> < 
> maker_errors 
> .log 
> ><repeat_masker_errors.log><repeat_masker_output.log><ATT00001.txt>

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