Make.biom with 5 columns of metadata

Commands in mothur
1

I want to make a biome table and I have sample information as follows in a file called “design.table”:

SampleID Animal# T1 T2 Tissue
Samp_1 Def-1 PCD14/21 PBCD4 Duodenum
Samp_2 Def-1 PCD14/21 PBCD4 Jejunum
Samp_3 Def-1 PCD14/21 PBCD4 Ileum
Samp_4 Def-1 PCD14/21 PBCD4 Colon
Samp_5 Def-2 PCD14/21 PBCD4 Duodenum
Samp_6 Def-2 PCD14/21 PBCD4 Jejunum

When I tried to use this with “make.biom” command with “metadata = design.table”, it gives the following error:
[ERROR]: expected 4 items of data for sample Samp_17 read 5, quitting.
[ERROR]: expected 4 items of data for sample Samp_18 read 5, quitting.
[ERROR]: expected 4 items of data for sample Samp_19 read 5, quitting.
[ERROR]: expected 4 items of data for sample Samp_20 read 5, quitting.
[ERROR]: expected 4 items of data for sample Samp_21 read 5, quitting.

When I tried with just one column, it worked fine. Does this mean I can only have one additional column with samples info?

2

Could you email your files to mothur.bugs@gmail.com so I can troubleshoot the issue?

3

Hi There,

I am having the same problem as the original user. My metadata file (which is essentially a txt file with lots of extra sample information in it) is causing errors when I try to make a biom file with metadata as an option. The .biom file is created fine when only the shared and constaxonomy options are included. The error is a a repetition of : ‘expected 372 items of data for sample V194 read 102, quitting’ for each of my samples. Is it possible that mothur has an issue loading a file with missing data as there is a fair amount of this in my file?

Many thanks for any help with this!

4

If you could create a new thread and ask your question there that would be great. Also if you could post the first few lines of your design file with the exact error message you are getting that would help us out.

Pat