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

[Carson Holt]

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 <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>

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