Error during running command

Commands in mothur
1

Dear all
I encounter a problem during running the command make.shared
I used the command make.shared to create .shared file from my biom table.

My syntax was
mothur > make.shared(biom=C1_otu_table_L3_min_3.biom)

These error message came.
[ERROR]: you file does not have a type provided.
[ERROR]: you file does not have a matrix_type provided.
[ERROR]: you file does not have a matrix_element_type provided.
[ERROR]: you file does not have a rows provided.
[ERROR]: you file does not have a columns provided.
[ERROR]: you file does not have a shape provided.
[ERROR]: you file does not have a data provided

Please suggest what should I will do.

2

I’d be happy to help. Could you post your biom file?

3

thanks @westcott for your reply. But I am unable to upload my .biom file as these is no option to upload a file.

I have analysed my metagenome data through qiime1 pipeline. Then use the command filter otus from otu tables.py to filter my desired otus.

4

If you send the biom file to mothur.bugs@gmail.com, I can take a closer look for you.

5

Thanks for sending your file. The issue is the biom file is in hdf5 format. You can extract shared files from hdf5 formatted biom files using the biom.info command.

mothur > biom.info(biom=C1_otu_table_L3_min_3.biom, format=hdf5)

6

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.