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rprops / PICRUSt_from_mothur

Guidelines for running PICRUSt with mothur biom output
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KeyError: "Unable to open object (object 'group-metadata' doesn't exist)" #2

Open adimascf opened 1 year ago

adimascf commented 1 year ago

Hello @rprops, thank you for making this guide. However, I got this KeyError when run biom convert command.

biom convert --table-type="OTU table" -i stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.opti_mcc.0.03.biom -o your_OTU_table.txt --to-tsv --header-key taxonomy

Traceback (most recent call last): File "/home/adimascf/miniconda3/bin/biom", line 8, in sys.exit(cli()) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(args, **kwargs) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/biom/cli/table_converter.py", line 113, in convert table = load_table(input_fp) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/biom/parse.py", line 671, in load_table table = parse_biom_table(fp) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/biom/parse.py", line 396, in parse_biom_table return Table.from_hdf5(file_obj, ids=ids, axis=axis) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/biom/table.py", line 4131, in from_hdf5 obs_ids, obs_md, obs_grp_md = axis_load(h5grp['observation']) File "/home/adimascf/miniconda3/lib/python3.9/site-packages/biom/table.py", line 4128, in axis_load for cat, val in grp['group-metadata'].items()} File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/home/adimascf/miniconda3/lib/python3.9/site-packages/h5py/_hl/group.py", line 328, in getitem oid = h5o.open(self.id, self._e(name), lapl=self._lapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5o.pyx", line 190, in h5py.h5o.open KeyError: "Unable to open object (object 'group-metadata' doesn't exist)"

Any help will be appreciated. Thank you.