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Problem with building the reference database
#1
Hi,
I am experiencing a problem when trying to build a reference database (→ wolf tutorial).

Using

obiconvert --embl -t ./TAXO --ecopcrdb-output=embl_last ./EMBL/*.dat

generates the error messages

ValueError: too many values to unpack
Exception AttributeError: "'EcoPCRDBSequenceWriter' object has no attribute '_file'" in <bound method EcoPCRDBSequenceWriter.__del__ of <obitools.ecop

See full output below. Any suggestions what might be the cause and how to fix it? Thanks!

full output:


robert@vfm-d023:~/wolf_tutorial2$ obiconvert --embl -t ./TAXO --ecopcrdb-output=embl_last ./EMBL/*.dat
Reading taxonomy dump file...
List all taxonomy rank...
Indexing taxonomy...
Indexing parent and rank...
Adding scientific name...
Traceback (most recent call last):
File "/home/robert/obitools/OBITools-1.2.9/export/bin/obiconvert", line 43, in <module>
writer = sequenceWriterGenerator(options)
File "/home/robert/obitools/OBITools-1.2.9/lib/python2.7/site-packages/obitools/format/options.py", line 364, in sequenceWriterGenerator
writer=EcoPCRDBSequenceWriter(options)
File "/home/robert/obitools/OBITools-1.2.9/lib/python2.7/site-packages/obitools/ecopcr/sequence.py", line 72, in __init__
self._taxonomy= loadTaxonomyDatabase(options)
File "/home/robert/obitools/OBITools-1.2.9/lib/python2.7/site-packages/obitools/ecopcr/options.py", line 78, in loadTaxonomyDatabase
taxonomy = TaxonomyDump(options.taxdump)
File "/home/robert/obitools/OBITools-1.2.9/lib/python2.7/site-packages/obitools/ecopcr/taxonomy.py", line 424, in __init__
for taxid,name,classname in self._nameIterator('%s/names.dmp' % taxdir):
File "/home/robert/obitools/OBITools-1.2.9/lib/python2.7/site-packages/obitools/ecopcr/taxonomy.py", line 526, in _nameIterator
for taxid,name,unique,classname,white in names:
ValueError: too many values to unpack
Exception AttributeError: "'EcoPCRDBSequenceWriter' object has no attribute '_file'" in <bound method EcoPCRDBSequenceWriter.__del__ of <obitools.ecop
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#2
This sounds very strange. The error indicates that the structure of the binary taxonomy files are not correct but the files seem to be correctly generated at the beginning of the command. It look like a bug, but I am surprised that such bug could exist on a so central part of the code.
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#3
In the TAXO directory, have you a set of files corresponding to a ncbi taxonomy dump ?
Whatever, can you download a new taxdump file from ncbi, to check if it solve the problem?
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#4
(10-11-2016, 05:15 AM)coissac Wrote: In the TAXO directory, have you a set of files corresponding to a ncbi taxonomy dump ?
Whatever, can you download a new taxdump file from ncbi, to check if it solve the problem?

Hi Eric,
I tried with a new download of the taxdump from NCBI; same error es before. In the EMBL folder I have the rel_std_mam01_r129.dat file from EMBL.
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