Error Loading BIOM to MEGAN6


#1

Hi, dear M. Community.

I was able to import BIOM files (from qiime) to MEGAN6 till now.
I recently update the MEGAN version and now I’m having an issue when trying to import same biom files that I exported before:

“Execute failed:java.io.IOException: Too many rows.shape=30289, 54”.

Please, I appreciate you kind help.
I have both JDK and KRE, plus openjfx software installed.

Thanks.


#2

Unfortunately, the BIOM “format” is not really a format, as the authors of the format never made an effort to specify how exactly to report different types of data.
To try and address this problem, MEGAN uses a heuristic to try and determine whether the data inside a BIOM file might be a taxonomic profile. Your file contains 30289 rows of data, which is what MEGAN will interpret as different samples. Because this number is to big, MEGAN rejects your request to open the file.
I presume that you don’t have 30289 samples, but rather your rows reflect perhaps OTUs?
If you give me access to the file then I will take a look at it…


#3

Hi, Daniel.

Sure, I understand.
I converted my biom file to ‘tsv’ to check out what you said about OTUs number instead of rows as samples. Rows are OTUs and Columns are samples.

(file deleted)

I appreciate your kind help.


#4

Hi, Daniel.

#An update.

I installed a previous version of MEGAN6 (V6.10.10 built 14/02/2018) and I’m able to import the same biom file I tried to import earlier.

Error was shown using the latest version (I guess): v6.11.4 built 08/05/2018.

Thanks,
K.


#5

Thanks for your input. I took a look at your file and this issue will be fixed in the next release of MEGAN.


#6

Thanks Daniel. For your time.

I’ll be working with the previous version until new one is released.

With gratitude,
K.