mothur

make biom.file to use this for core.diversity in QIIME

Hi

I have used mothur (miseq sop) for illumina paired-end reads and want to make a biom.file and use this in QIIME.
I used the following commands in mothur to create the biom.file:

make.biom(shared=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.gg.an.unique_list.shared, constaxonomy=stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.gg.an.unique_list.0.03.cons.taxonomy)

This worked fine. The output: stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.gg.an.unique_list.0.03.biom

was used in QIIME using this command (using Macqiime):
core_diversity_analyses.py -i stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.gg.an.unique_list.0.03.biom -o finland_core_project2b -m M2.txt -e 5951 --nonphylogenetic_diversity --suppress_group_significance

I got the following error message:

Traceback (most recent call last):
File “/macqiime/anaconda/bin/core_diversity_analyses.py”, line 202, in
main()
File “/macqiime/anaconda/bin/core_diversity_analyses.py”, line 199, in main
status_update_callback=status_update_callback)
File “/macqiime/anaconda/lib/python2.7/site-packages/qiime/workflow/core_diversity_analyses.py”, line 228, in run_core_diversity_analyses
close_logger_on_success=False)
File “/macqiime/anaconda/lib/python2.7/site-packages/qiime/workflow/util.py”, line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Filter low sequence count samples from table (minimum sequence count: 5951)
Command run was:
filter_samples_from_otu_table.py -i stability.file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.gg.an.unique_list.0.03.biom -o finland_core_project2b/table_mc5951.biom -n 5951
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
File “/macqiime/anaconda/bin/filter_samples_from_otu_table.py”, line 162, in
main()
File “/macqiime/anaconda/bin/filter_samples_from_otu_table.py”, line 138, in main
write_biom_table(filtered_otu_table, output_fp)
File “/macqiime/anaconda/lib/python2.7/site-packages/qiime/util.py”, line 577, in write_biom_table
biom_table.to_hdf5(biom_file, generated_by, compress)
File “/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py”, line 3535, in to_hdf5
self.group_metadata(axis=‘observation’), ‘csr’, compression)
File “/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py”, line 3507, in axis_dump
formatter[category](grp, category, md, compression)
File “/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py”, line 243, in general_formatter
compression=compression)
File “/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/group.py”, line 99, in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
File “/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.py”, line 60, in make_new_dset
raise ValueError(“Shape tuple is incompatible with data”)
ValueError: Shape tuple is incompatible with data

Does anyone know what I am doing wrong?

Thank you very much :slight_smile:

Kristin

Sorry, but we don’t provide support for QIIME and I suspect it would be too difficult for us to dig into their code to figure out what is going wrong on our end or theirs. Why not run you diversity analysis in mothur using summary.single or summary.shared?

Pat