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WFSRDataScience / PIMENTA

PIMENTA for rapid identification of species using MinION sequencing
https://pimenta.readthedocs.io
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Documentation Seems to be Lacking #3

Closed MycoMap closed 1 month ago

MycoMap commented 6 months ago

in the settings file, there is no explanation on what is required for the following:

MARKERS TO ANALYSE

Targets=""

File containing marker primer sequences

PrimerFile=

MycoMap commented 6 months ago

FIrst attempt to run failed because dos2unix was not installed. sudo apt install dos2unix

MycoMap commented 6 months ago

Stuck here:

Run_DNA-metabarcoding-MINION.ITSFungal.sh: line 170: module: command not found Run_DNA-metabarcoding-MINION.ITSFungal.sh: line 171: module: command not found

MycoMap commented 6 months ago

Also I do not see an input for a barcode/index file. Does this only work with ONT barcodes?

valerievandervorst commented 6 months ago

Hi,

There is a readthedocs website dedicated to PIMENTA of which the link is also included in the "About" section of this repository: https://pimenta.readthedocs.io/en/latest/

valerievandervorst commented 6 months ago

Stuck here:

Run_DNA-metabarcoding-MINION.ITSFungal.sh: line 170: module: command not found Run_DNA-metabarcoding-MINION.ITSFungal.sh: line 171: module: command not found

It seems I still included the fix for the HPC I use, I for now removed this part. It should not cause an issue for the pipeline, this fix tried to reload a (slurm) module, but is not required.