Error using MetONTIIME - Missing fromPath parameter

Hi All,

I have used QIIME2 alot but generally with Illumina data. I am not attempting to use MetONTIIME for nanopore through nextflow, but keep hitting the same error.

Launching [wise_swartz] DSL2 - revision: 3a67d1d68a
Missing fromPath parameter

I have had a look through both the .conf and .nf files (attached below) and can't see what I have done wrong in the configurations. Could someone who has done this before have a look and tell me where I am going wrong.

Kind regards
metontiime2_conf.txt (9.8 KB)
metontiime2_nf.txt (26.8 KB)

Hi @Rebekah_Henry1,
Welcome to the QIIME 2 Forum! None of our developers have experience with MetONTIIME (it's not developed by us), but I just shared your post with the MetONTIIME developer in the hope that they can answer your question.

Thanks for your interest in QIIME 2!


Dear @Rebekah_Henry1,
I think there are two main issues in the config file. First, since your files are in /fs03 folder, you should make it accessible to either docker or singularity containers.
To do so, if you are using singularity profile, you should edit line 74 from:
containerOptions = '--bind /home/:/home'
containerOptions = '--bind /home/:/home --bind /fs03:/fs03'

While, if you are using docker profile you should edit line 171 from:
containerOptions = '-v /home/:/home'
containerOptions = '-v /home/:/home -v /fs03:/fs03'

Second, I saw you probably already have qza files for both sequences and taxonomy. If that is the case, they should be put in /fs03/pv54/Beks/Raw-Reads/nanopore_silvan/run1_metontiime/importDb folder with files names specified by dbSequencesQza and dbTaxonomyQza parameters, respectively, and the importDb process (line 53) should be set to false with:
importDb = false
While, if you would like to start from fasta and tsv files, it's ok to leave the importDb process set to true and you should specify the full path to those files as values for dbSequencesFasta and dbTaxonomyTsv parameters.
I hope this solves your issue, but if you have any further questions, please open an issue in the GitHub repository.
P.s.: I would suggest first testing the pipeline configuration with the demo dataset uploaded in the repo.


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