Hello
I'm using Qiime2 on Ubuntu
and I'm trying to import some demultiplexed data using the following command:
qiime tools import
--type "SampleData[SequencesWithQuality]"
--input-path /home/kalonji/microbiome_studies/Barley_Microbiome/qiime2_16_Demux/demux/manifest.csv
--input-format SingleEndFastqManifestPhred33v2
--output-path /demux-single-end.qza
And I'm getting the following error :
There was a problem with the command:
(1/1) Missing option '--output-path'.
(qiime2) kalonji@kalonji-Precision-T7610:~/microbiome_studies/Barley_Microbiome$ --input-format SingleEndFastqManifestPhred33v2 \
--output-path /demux-single-end.qza
The manifest data is like this:
Sample-id,Absolute-filepath,direction
BCH1,$PWD/home/kalonji/microbiome_studies/Barley_Microbiome/qiime2_16_Demux/demux/BCH1_S1_L001_R1_001.fastq.gz,forward
And I saved it as a csv file
i'm new to this, any assistance will be highly appreciated
Thanks
I think the command is missing the \ backslash \ that tells it to continue the same command on a new line. In this example from the tutorial, the backslashes are used to continue the one import command over five lines.
Make sure your manifest files exactly match the format of the importing data examples, including capitalization! Linux software, including Qiime2, Cares A Lot About Capitalization, so make sure to make it matches to avoid any errors.