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

[Hayley Mangelson]

I am working on an AWS EC2 instance that runs Amazon Linux, and I have
tried a couple of installs (MPICH and Open MPI), neither of which worked. I
don't have any installed on my current instance.

On Tue, Aug 15, 2023 at 5:08 PM Carson Holt <carsonhh at gmail.com> wrote:

> Do you already have MPI installed on your system, and if so which MPI and
> what version (i.e. MPICH, MVAPICH2, Intel MPI, Open MPI, etc)?
>
> —Carson
>
>
> On Aug 15, 2023, at 9:34 AM, Hayley Mangelson <hayley at phasegenomics.com>
> wrote:
>
> 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
>
>
>

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