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 
Kristin