mothur

Error during running command

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.

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

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.

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

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)

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