Run IMP with testdataset
I tried to run IMP with the test dataset obtained from here.
My config file looks like this:
{
"threads": 24,
"memory_total_gb": 200,
"memory_per_core_gb": 200,
"outputdir": "/data/testdata/output/",
"raws": {
"Metagenomics": "/data/testdata/raw_data/metagenomics/",
"Metatranscriptomics": "/data/testdata/raw_data/metatranscriptomics/"
},
"assembler": "idba",
"vizbin": {
"perp": 10,
"cutoff": 1
}
}
$ tree testdata/
testdata/
├── config.json
└── raw_data
├── metagenomics
│ ├── mg.r1.fq
│ └── mg.r2.fq
└── metatranscriptomics
├── mt.r1.fq
└── mt.r2.fq
If I try to run IMP, I get the following error:
$ impy -c /data/testdata/config.json run
You should provide `metagenomics` and `metatranscriptomics` data.
Aborted!
Am I doing something wrong to access the config file?
(I am aware that I don't need 24 threads and 200GB of memory for this dataset, but I have problems with another dataset and I am trying to find out if the computational ressources are a problem).