Dear devs, dear users
I am processing metagenome dataset. I currently follow the q2-moshpit: A set of tutorials showcasing shotgun metagenomics analysis workflows, but I modified some steps.
I assembled metagenomes and binned samples outside of Qiime2. So, for each sample, I have bins that are not dereplicated and not filtered. My plan is to import all the bins together into Qiime2, filter them, and then dereplicate.
Here is the command:
qiime tools cache-import \
--type 'SampleData[MAGs]' \
--input-path Bins_pooled \
--cache ./cache \
--input-format 'MultiMAGSequencesDirFmt' \
--key 'pooled_bins'
Error I got:
There was a problem importing Bins_pooled:
Missing one or more files for MultiMAGSequencesDirFmt: 'MANIFEST'
As I understood, I need the manifest file. And I can't find relevant information:
- Should it be located in the "Bins_pooled" directory?
- What is the structure of this file?
Unfortunately, I couldn't find an example artifact to inspect. I would appreciate it if somebody shared the artifact, manifest file, or instructions on how to import bins/mags into qiime2.
Best,
Timur