obi annotate
Hi everyone, I would like to annotate a ecopcr output with taxonomic information. I tried this: obi annotate --with-taxon-at-rank kingdom --with-taxon-at-rank phylum --with-taxon-at-rank class --with-taxon-at-rank order --length --taxonomy vert01/TAXONOMY/my_tax vert01/12S_refs_uniq_clean vert01/12S_refs_uniq_clean_annotated
obtaining this output
2021-02-10 16:17:25,640 [annotate : INFO ] obi annotate Reading 2308086 taxa... No local taxa Indexing taxon names... 0.0 % |/ ] remain : 00:44:58DEBUG /tmp/pip-install-kkel6je8/obitools3_0d90d2c93d2149d680e4178f2ccc12c8/src/encode.c:345:encode_seq_on_4_bits, obi_errno = 24, errno = 2 : Invalid nucleotide base when encoding (not IUPAC), sequence: Pleuronectiformes Traceback (most recent call last): File "python/obitools3/commands/annotate.pyx", line 367, in obitools3.commands.annotate.run File "python/obitools3/commands/annotate.pyx", line 190, in obitools3.commands.annotate.sequenceTaggerGenerator.sequenceTagger File "python/obitools3/dms/view/view.pyx", line 790, in obitools3.dms.view.view.Line.setitem File "python/obitools3/dms/column/typed_column/seq.pyx", line 68, in obitools3.dms.column.typed_column.seq.Column_seq.set_line File "python/obitools3/dms/column/typed_column/seq.pyx", line 80, in obitools3.dms.column.typed_column.seq.Column_seq.set_line File "python/obitools3/utils.pyx", line 100, in obitools3.utils.obi_errno_to_exception Exception: Problem setting a value in a column
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/petroni/Scrivania/Gabriele/obi3-env/bin/obi", line 62, in config[root_config_name]['module'].run(config) File "python/obitools3/commands/annotate.pyx", line 370, in obitools3.commands.annotate.run obitools3.dms.view.view.RollbackException: obi annotate error, rollbacking view: Problem setting a value in a column
I can see that a sequence results as problematic, since it has non IUPAC bases, but I don't know how to solve it. I exported the database (.csv) which I'd like to annotate, to look for the defective sequence, but the database is composed by just two columns, one with the genbank A.N. and the other with the relative sequence. What am I doing wrong? G 12S_db_97.rar