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.
metontiime2.nf [wise_swartz] DSL2 - revision: 3a67d1d68a
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.
metontiime2_conf.txt (9.8 KB)
metontiime2_nf.txt (26.8 KB)
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!
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
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
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.