DeniRibicic

@ondovb It's a melted Phyloseq (uses biom format) object. Basically it is a long data format when melted. There is a sample, abundance and different taxonomy level columns. ``` Sample...

Hi @roblanf, I am experiencing very similar error to one that @avantonder posted: ``` INFO [2020-04-13 13:22:27] Loading input file: 0_basecalled/sequencing_summary.txt INFO [2020-04-13 13:22:32] MinION flowcell detected INFO [2020-04-13 13:22:34]...

@roblanf all the packages were up-to-date, but R was an older version `R version 3.5.1 (2018-07-02) -- "Feather Spray"` Updating to recent version solved the problem `R version 3.6.3 (2020-02-29)...

@roblanf something interesting is happening. When I run the script directly in my shell everything works fine. However, I have incorporated the `MinIONQC.R` in my workflow through a `bash` script...

@roblanf sorry for the late reply. Here is some info: ``` SHELL=/bin/bash SSH_CLIENT=10.218.129.55 55285 22 CONDA_SHLVL=1 CONDA_PROMPT_MODIFIER=(base) LC_NUMERIC=nb_NO.UTF-8 SSH_TTY=/dev/pts/23 CONDA_EXE=/home/denir/anaconda3/bin/conda DESKTOP_MODE=1 _CE_CONDA= CONDA_BACKUP_JAVA_HOME= MAIL=/var/mail/denir PATH=/home/denir/bin:/home/denir/anaconda3/bin:/home/denir/anaconda3/condabin CONDA_PREFIX=/home/denir/anaconda3 SHLVL=1 HOME=/home/denir Ubuntu 16.04...

You have your output, meaning nothing is wrong there. If you read carefully the pipeline description, you will learn that the vsearch is clustering OTUs based on 85% similarity, which...

It's version 9. I actually needed only classifier, and I have installed it through anaconda. So, I am okay now. However, the whole tools installation as specified in your repository...