"seq 0 in refs view has no taxid associated" while building custom reference database
I am building my own reference database, and all steps seem to work except the last step with
(.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)?