[maker-devel] MAKER Commercial User -- Install and run issues

[Hayley Mangelson]

Hi Carson,

Excellent, thanks so much! I have that part working. The multithreading is
still eluding me. Do you have a recommended method of installing a
compatible version of MPI?

Thanks,

Hayley

On Fri, Aug 11, 2023 at 4:04 PM Carson Holt <carsonhh at gmail.com> wrote:

> The error is coming from Augustus. There is a problem with the species
> file you selected. Or you put it in the wrong place.
>
> This is the error —>
> Could not find the config file
> /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg
>
> The species info must exist under this base directory by default (it’s
> where you let MAKER install Augustus) —>
>  /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/
>
> You can also place the species files somewhere else but you need to set
> the AUGUSTUS_CONFIG_PATH so Augustus knows where to look.
>
> Example (in your ~/.bash_profile):
> export AUGUSTUS_CONFIG_PATH=$HOME/muy_augustus_species
>
> Thanks,
> Carson
>
>
>
> On Aug 11, 2023, at 7:20 AM, Hayley Mangelson <hayley at phasegenomics.com>
> wrote:
>
> Hi Carson,
>
> Sure thing! Sorry for the delay, I was on vacation. I reran with just a
> single scaffold. Here is the STDERR.
>
> On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <carsonhh at gmail.com> wrote:
>
>> Can you send me the STDERR from the maker run? If you don’t have it, run
>> maker again with the output from the screen redirected to a file. Example
>> —> maker &> all_output.txt
>>
>> --Carson
>>
>> Sent from my iPhone
>>
>> On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <hayley at phasegenomics.com>
>> wrote:
>>
>> 
>> Hi!
>>
>> I am trying to get a fresh install of MAKER to work for me and am having
>> a few issues.
>>
>> 1. I got MAKER installed (I thought) and now the log is saying all
>> contigs failed. See attached log.
>> 2. Having tried several versions and methods of installation, I cannot
>> get multithreading to work.
>>
>> Could you help me work through these issues?
>> Thanks,
>>
>> Hayley
>> --
>> Hayley Mangelson
>> Senior Bioinformatics Lead
>> Phase Genomics, Inc
>> www.phasegenomics.com
>>
>> <PGA_assembly_hap1_master_datastore_index.log>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
> --
> Hayley Mangelson
> Senior Bioinformatics Lead
> Phase Genomics, Inc
> www.phasegenomics.com
>
> <all_output.txt>
>
>
>

-- 
Hayley Mangelson
Senior Bioinformatics Lead
Phase Genomics, Inc
www.phasegenomics.com
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