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Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS
http://bioinf.uni-greifswald.de/webaugustus/
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Unable to locate command line parameters file #412

Closed katieemelianova closed 3 months ago

katieemelianova commented 3 months ago

Hi there,

I am running Augustus within MAKER and am running into an issue, perhaps you can help.

I am running maker as follows, setting the environment variables show:

export LIBDIR=/lisc/app/repeatmasker/4.1.6-3.12.4-5.40.0/Libraries/
export REPEATMASKER_LIB_DIR=/lisc/app/repeatmasker/4.1.6-3.12.4-5.40.0/Libraries/
export AUGUSTUS_CONFIG_PATH=/lisc/scratch/botany/katie/annotation/local_augustus_config/config
mpiexec -n 32  /lisc/app/conda/miniconda3/envs/maker-3.01.03/bin/maker -cpus 32 -base round2 maker_opts_round2.ctl maker_bopts.ctl maker_exe.ctl

The AUGUSTUS_CONFIG_PATH seems to contain all the folders that I need:

ls /lisc/scratch/botany/katie/annotation/local_augustus_config/config
cgp  extrinsic  model  parameters  profile  species

But when I run maker via slurm, not all the folders from the config seem to be copied across to the temporary slurm directory:

ls /lisc/slurm/node-d13/tmp/slurm-1874997/maker_Z8t_BU/augustus_config/19f87e9215aab674891f3238099dc663/
extrinsic  model  profile  species

Resulting in an error from Augustus during MAKER:

/lisc/app/conda/miniconda3/envs/augustus-3.5.0/bin/augustus: ERROR
Could not locate command line parameters file: /tmp/slurm-1874997/maker_Z8t_BU/augustus_config/19f87e9215aab674891f3238099dc663/parameters/aug_cmdln_parameters.json.

I'm not sure if this is a Augustus problem or a slurm problem - could you recommend any way to debug or suggest what could be happening?

Thanks in advance for your help :)

Best,

Katie

MarioStanke commented 3 months ago

It is not a slurm problem. A couple of years ago we have introduced config/parameters/aug_cmdln_parameters.json so pygustus can use the same command line parameters as augustus in C++.

I suspect that MAKER copies some directories explicitly where it should probably copy all config subdirectories except irrelevant parts of species (to save space). Or one could add the parameters subdirectory to the list of paths to copy.

If that is true it should be fixed in MAKER, but I am not sure whether it is still maintained.

katieemelianova commented 3 months ago

Hi Mario,

Thanks a lot for the explanation - it doesn't look like maker is under active development unfortunately.

Best,

Katie

rongrongy commented 2 months ago

Hi, guys I had the same problem as you, may I ask if you have solved it by now.