Importing biom format.. qiime 1.9.1 output files

User Questions
1

Dear Daniel,
I feel somehow MEGAN is not being able to import new qiime 1.9.1 version output files. Can you please check? Previous 1.8.0 version output files works perfectly with MEGAN for the same data.
If you need I can send you the .biom file. Please let me know.
Thank you,
Suparna

2

Please send me an example and I will look at it. Also, would biom2 format help?

3

I have sent you using mail reply option. Hope you got it? Also to add that qiime 1.8.0 output file worked perfectly, but not the 1.9.1 version. Input was the same fasta file.
Thanks.S

4

Dear Daniel,
I had a discussion with the qiime group, they updated their .biom file format from qiime 1.9.1 and the “otu_table.biom” is encoded using the HDF format. This is a compressed, binary format, which is why it’s not human readable. And thus “less” or “head” didn’t work also megan import is not working.
The HDF format is only usable by qiime 1.9 and qiime 2.
I sent you the example otu_table.biom file created with 1.9.1 version (together with the old 1.8.0 version which megan reads well)
Can you please make megan compatible with this so that it can read these files?
Thanks a lot,
suparna

5

Hi Suparna, sounds like they have switched to Biom2 format. MEGAN currently only can parse biom1 format, but there is a program out there that can convert biom2 to biom1.
Implementing biom2 is on my list of things to do…

6

Hi Suparna, I can’t find the email with your biom2 format file. Please resend it to me, as I am now working on implementing a biom2 parser…

1 Like
7

Hi Suparna, I have implemented a first version of BIOM2 import in MEGAN and it will be available in the next release. Unfortunately, the BIOM2 format is poorly documented and also there do not seem to be an example files for most of the formats indicated features, so I anticipate the need to update my implementation as people try using it with files that contain some of the those undocumented (or under documented) features.