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

[Carson Holt]

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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <http://www.phasegenomics.com/>
>>>>> 
>>>>> <PGA_assembly_hap1_master_datastore_index.log>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at yandell-lab.org <mailto: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 <http://www.phasegenomics.com/>
>>> 
>>> <all_output.txt>
>> 
> 
> 
> -- 
> Hayley Mangelson
> Senior Bioinformatics Lead
> Phase Genomics, Inc
> www.phasegenomics.com <http://www.phasegenomics.com/>
> 

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