importing DNA sequence data

Technical Support
,
#1

i’m trying to Importing DNA sequence data into QIIME 2 and creating a visual summary. i created the manifest file and insert the sample names into the sample-id column and add the full paths to the sequence files in the absolute-filepath column. i have encounter with this error when i used the manifest file to import the sequences into QIIME 2:
qiime tools import \

--input-path manifest.tsv \
--type 'SampleData[SequencesWithQuality]' \
--input-format SingleEndFastqManifestPhred33V2 \
--output-path se-demux.qza

qiime: command not found
can you please help me with this?

#2

Hi!
Are you sure you did not forget to activate qiime2 environment before running the command? Or could you provide a screen of your terminal window?

1 Like
#3

Thanks for your kindness and support. I used your comment to activate qiime2 environment via this command and so far no locale errors.:

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml
conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2020.11-py36-linux-conda.yml

conda activate qiime2-2020.11

conda install -c conda-forge jupyterlab

jupyter serverextension enable --py qiime2 --sys-prefix

conda install -c conda-forge nodejs #may need to force a specific version if build fails

jupyter lab build