GitLab

Hi,

I am building my own reference database, and all steps seem to work except the last step with obi build_ref_db.

(.venv_obi3) ahaegeman@genomics2:/home/genomics/ahaegeman/eDNA/Test_OBITools3$ obi build_ref_db -t 0.97 --taxonomy dms/taxonomy/taxdump dms/Riaz_Feb2020_amp_clean_uniq dms/Riaz_Feb2020_db_97
2020-02-24 11:12:30,168 [build_ref_db : INFO ]  obi build_ref_db
Building kmer tables... : Done
Done : 100 %
Reading 2226902 taxa...
No local taxa
DEBUG /tmp/pip-build-5mt4_c3y/OBItools3/src/build_reference_db.c:229:build_reference_db, obi_errno = 0, errno = 2 :
Error getting a taxid when building a reference database, seq 0 in refs view has no taxid associated
Traceback (most recent call last):
  File "/home/genomics/ahaegeman/.venv_obi3/bin/obi", line 68, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/build_ref_db.pyx", line 85, in obitools3.commands.build_ref_db.run
Exception: Error building a reference database

According to the error message there seems to be a sequence with no taxid associated, although in my input fasta all sequences have an associated taxid (the same fasta is also used succesfully in the OBITools1 workflow).

Is there any way to check the result of the obi uniq command visually to see if something is missing there (for example export this to a fasta file)?

Kind regards,

Annelies