Error uploading data

MicrobiomeAnalyst
1

Hi!

I’m trying to upload abundance data generated from metagenomic shotgun sequencing. It is a csv file. I’m getting the following error:

Error!

Possible causes of error (last one being the most relevant):

Errors in parsing your data as numerics - possible reason: comma as decimal separator?

I’ve checked and commas are not being used as a decimal separator. I also get the same error when I try using the example mouse_colitis.txt dataset.

Here is a sample of the data set I am using:

#NAME,Sample_E,Sample_D,Sample_B,Sample_A,Sample_C,Sample_F,Sample_P,Sample_O,Sample_N,Sample_M,Sample_L,Sample_K,Sample_J,Sample_I,Sample_H,Sample_G
#GROUP,nAB,nAB,AB,AB,nAB,nAB,AB,nAB,nAB,AB,AB,AB,AB,AB,AB,AB
Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanobrevibacter;Methanobrevibacter_smithii,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanosphaera;Methanosphaera_stadtmanae,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinobaculum;Actinobaculum_massiliense,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;Actinomyces_cardiffensis,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;Actinomyces_europaeus,0,0,0,0,0,0,0,0,0,0,0,0,0,0.02965,0,0
Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;Actinomyces_odontolyticus,0,0,0,0,0,0,0,0,0,0,0,0.00756,0,0,0,0.00772

Cheers,
Sophie

2

Please provide the missing information as described in this post

3

Hi,

Sorry!
Shotgun data profiling > a gene abundance table > Gene ID Type: Other gene annotation > abundance file: mouse_colitis.txt > metadata file: none

Example dataset: mouse_colitis.txt (downloaded from https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/resources/data/mouse_colitis.txt)

4

Hello, the problem is that you need to separate the meta file from the abundance table.
As indicated in the upload webpage, two separate tables are required for further processing. Please find the right format by hanging on the question mark.

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image1590×710 48.3 KB

Hope this helps.
Best

5

I can see two clear issues:

  1. The abundance file you used is for Marker Gene Profile module
  2. The meta-data is missing

At the data upload page (shown above), go to “Try our examples” tab to see the expected data files