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I am running the tutorial to make a custom reference database described here.

After solving the problems in #76 (closed) i ran obi ecopcr successfully, then obi grep to require a taxonomic assignment at genus and family level and then obi uniq with the following command:

obi uniq --taxonomy /Volumes/Elements/EMBL_dms/taxonomy/my_tax /Volumes/Elements/EMBL_dms/COI_BF3_BR2_clean /Volumes/Elements/EMBL_dms/COI_BF3_BR2_uniq

which failed after ~8h with the following error:

    2020-04-11 00:20:22,927 [uniq : INFO ]  obi uniq
    Reading 2238873 taxa...
    No local taxa
    2020-04-11 00:20:26,244 [uniq : INFO ]  First browsing through the input
    100.0 % |##################################################/] remain : 00:00:00
    2020-04-11 00:44:58,260 [uniq : INFO ]  Second browsing through the input
    86.4 % |###########################################\       ] remain : 02:00:38DEBUG /Applications/OBITools/obitools3/src/obidmscolumn.c:1994:obi_enlarge_column, obi_errno = 18, errno = 28 : 
    Error enlarging a column file
    Traceback (most recent call last):
    File "python/obitools3/commands/uniq.pyx", line 550, in obitools3.commands.uniq.run
    uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
    File "python/obitools3/commands/uniq.pyx", line 399, in obitools3.commands.uniq.uniq_sequences
    o_view[o_idx] = u_seq
    File "python/obitools3/dms/view/view.pyx", line 202, in keys
    yield col_alias
    File "python/obitools3/dms/view/view.pyx", line 741, in obitools3.dms.view.view.Line.__setitem__
    (self._view).get_column(column_name_b).set_line(self._index, value)
    File "python/obitools3/dms/column/typed_column/seq.pyx", line 68, in obitools3.dms.column.typed_column.seq.Column_seq.set_line
    cpdef set_line(self, index_t line_nb, object value):
    File "python/obitools3/dms/column/typed_column/seq.pyx", line 80, in obitools3.dms.column.typed_column.seq.Column_seq.set_line
    obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
    File "python/obitools3/utils.pyx", line 100, in obitools3.utils.obi_errno_to_exception
    raise Exception(None or error_message)
    Exception: Problem setting a value in a column
    During handling of the above exception, another exception occurred:
    Traceback (most recent call last):
    File "/Applications/OBITools/obitools3/obi3-env/bin/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
    File "python/obitools3/commands/uniq.pyx", line 552, in obitools3.commands.uniq.run
    raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
    obitools3.dms.view.view.RollbackException: obi uniq error, rollbacking view: Problem setting a value in a column