Evaluate bins with BUSCO in MOSHPIT tutorial 4.1.6 section

Technical Support
1

MANIFEST is not a(n) MultiMAGManifestFormat file

Dear all

I having issues to move to the next step in this MOSHPIT tutorial (https://moshpit.qiime2.org/_/downloads/en/2025.7.0/pdf/), I am running this code:
mosh annotate evaluate-busco
--i-mags ./cache:mags
--i-db ./cache:busco_db
--p-lineage-dataset bacteria_odb12
--p-cpu 32
--o-visualization /mags.qzv
--o-results ./cache:busco_results
--verbose

I got this error message:
MANIFEST is not a(n) MultiMAGManifestFormat file:

No sample records found in manifest, only observed comments, blank lines, and/or a header row.

Plugin error from annotate:

/MANIFEST is not a(n) MultiMAGManifestFormat file:

No sample records found in manifest, only observed comments, blank lines, and/or a header row.

I was tinking to modify the MANIFEST file and adapt the MANIFEST file to the MIltiMAGManifestFormat file format. Unfortunatelly I didnt find nothing helpful to move forward.

If its helpful, this is an example of my current MANIFEST header file:

sample-id,mag-id,filename
1163,0453259e-8e3b-4f09-a8cc-71307561ebe6,1163/0453259e-8e3b-4f09-a8cc-71307561ebe6.fasta
1163,178f605e-bce8-40a2-acba-70045480966f,1163/178f605e-bce8-40a2-acba-70045480966f.fasta
1163,218dc332-3ac1-4539-87e5-6ac6146fcd63,1163/218dc332-3ac1-4539-87e5-6ac6146fcd63.fasta
1163,244ba0b5-ae16-48c0-b00e-6c8c6d97d682,1163/244ba0b5-ae16-48c0-b00e-6c8c6d97d682.fasta

Everything is stored in a cache directory, as recommended at the beginning of the tutorial.
I appreciate any suggestions or comments.

1 Like
3

Hey @ferflei,

Sorry to hear you experienced this issue! From the documentation link you included I can see that you used the 2025.7 version of the docs - was your environment also 2025.7? If yes, would you mind trying the tutorial using the newest MOSHPIT version (2026.1)? We have patched up a few things here and there so perhaps that can help. If you still get an error, let us know and we'll do some more troubleshooting.

Thanks!

Cheers,
Michal

1 Like
6

Hi @misialq thanks for your answer.

Yes, the enviroment is 2025.7

I will update the version, then I will let you knwon if works or not.

Thanks!

Cheers.

Fernando.

1 Like
7

Dear @jakabaesj10

Thanks for your comments, I verified both Unix-style line endings and UTF-8 encoding. The manifest file looks is fine or what do you think? here the outputs that I ran:
file MANIFEST
MANIFEST: ASCII text

cat -A MANIFEST | head
sample-id,mag-id,filename$
1163,0453259e-8e3b-4f09-a8cc-71307561ebe6,1163/0453259e-8e3b-4f09-a8cc-71307561ebe6.fasta$
1163,178f605e-bce8-40a2-acba-70045480966f,1163/178f605e-bce8-40a2-acba-70045480966f.fasta$
1163,218dc332-3ac1-4539-87e5-6ac6146fcd63,1163/218dc332-3ac1-4539-87e5-6ac6146fcd63.fasta$

If you have another option ro veryfy Unix-style line endings and UTF-8 encoding please let me know.

Thanks.

Best.

Fernando.

8

Hi @misialq

I asked the technical team at the institution where I work to update the qiime-mospit version as you suggested. They are having issues installing the latest version (2026.4). It seems that version 2026.4 is not yet finalized, so they installed version 2026.1 instead. I ran my script again, but I got the same error. Do you think that using the latest version (2026.4) would make a difference?

Thaks for your comments.

Fernando.

9

Hey @ferflei,

Thanks for trying out the 2026.1 version. You are correct - the 2026.4 release is not finalized yet and should be available later this month but I am not sure this one would fix the issue. I will look into it a bit more and get back to you - sorry for the inconveniance!

Cheers,
Michal

1 Like