Importing bins/mags into Qiime2

[timanix (Timur Yergaliyev)]

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

[timanix (Timur Yergaliyev)]

Thanks to one researcher who uploaded the "mags.qza" file to their GitHub repo (and Google!), I was able to recreate the structure and import MAGs binned outside of qiime2 (the same command as above).
The folder should contain a "MANIFEST" file (comma separated, no extension) and subdirectoriy for each sample, with all MAGs binned for that sample (fasta format).

MANIFEST file:

sample-id,mag-id,filename
S1,bin1,S1/S1bin1.fasta
S1,bin2,S1/S1bin2.fasta
S2,bin1,S2/S2bin1.fasta
S2,bin2,S2/S2bin2.fasta

Best,

Please follow instructions here