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MaestSi / MetONTIIME

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
GNU General Public License v3.0
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COLLAPSE_TABLE PROCESS CREATES ONLY RESULTS FOR TAXONOMIC LEVEL1 #72

Closed dloukovi closed 1 year ago

dloukovi commented 1 year ago

WHEN RUNNING THE ANALYSIS, AFTER 'ASSIGNTAXONOMY' PROCESS IS COMPLETED, THE 'COLLAPSETABLE' PROCESS PRODUCES RESULTS ONLY FOR TAXONOMIC LEVEL 1. WHEN THE 'DIVERSITYANALYSIS' PROCESS FOLLOWS, IT CANNOT BE COMPLETED (ERROR) CAUSE IT CANNOT FIND ALL THE NECESSARY FILES (FILES FOR TAXONOMIC LEVEL6) IN THE COLLAPSE TABLES DIRECTORY

MaestSi commented 1 year ago

Hi, are you using a recent version of the pipeline? Which database are you using? Please provide the command you ran, the config file and error messages. SM

dloukovi commented 1 year ago

Dear Simone, I am using the latest version (with nextflow and docker). I managed to adjust configurations for docker (it was not so easy for a beginner in bioinformatics...). I used the NCBI16S database (the same that EPI2ME uses). If I disable the diversity analysis process in the config file, the process is completed but produces only collapsed tables for taxonomic level 1. That's why if I enable the diversity analysis (for level 6 in config file) it comes with an error 'cannot find feature table level 6 in collapse table dir'. I have attached the config file for your consideration.

dloukovi commented 1 year ago

here's the attachment.. metontiime2.zip .

MaestSi commented 1 year ago

Hi, I see in the config file that you set to false importDb process, is this because the import already succeeded. I suspect there could be issues in the formatting of the database you used, which prevent the pipeline from recognising the taxonomy levels. Could you also please provide a few lines of taxonomy tsv (and fasta) files you are using? Thanks, SM

MaestSi commented 1 year ago

Closing the issue due to inactivity.