Hi,
I have been using obitools for my analysis of 16S metabarcoding data. Just trying to create an ecoPCR database from the SILVA SSU database, prior to taxonomic assignment.
As per the manual, I have tried the following:
obisilva --ssu --parc --local=/home/silva_db
the folder silva_db contains:
SILVA_132_SSUParc_tax_silva.fasta
/taxonomy/tax_slv_ssu_132.txt
this executes fine and the progress bar shows 100% and I get the following output files:
-rw-rw---- 1 user user 2814245955 Sep 2 13:08 silva_132_ssuparc_full_001.sdx
-rw-rw---- 1 user user 162328 Sep 2 12:53 silva_132_ssuparc_full.adx
-rw-rw---- 1 user user 256770210 Sep 2 13:08 silva_132_ssuparc_full.ldx
-rw-rw---- 1 user user 637224 Sep 2 12:53 silva_132_ssuparc_full.ndx
-rw-rw---- 1 user user 296 Sep 2 12:53 silva_132_ssuparc_full.rdx
-rw-rw---- 1 user user 434319 Sep 2 12:53 silva_132_ssuparc_full.tdx
But it doesn't create a pdx file, which it looks for later on when using
ecotag -d silva_132_ssuparc_full -R SILVA_132_SSUParc_tax_silva.fasta input.fasta > output.fasta
Error message:
Reading binary taxonomy database...
[INFO : Taxon alias file found]
[INFO : Local taxon file found] : 6073181 added taxa
Taxonomical tree read
[Errno 2] No such file or directory: 'silva_132_ssuparc_full.pdx'
[INFO : Preferred taxon name file not found]
ok
Reading reference DB ... : 6073181
Traceback (most recent call last):
File "/usr/bin/ecotag", line 346, in <module>
taxonlink[seqid]=int(seq['taxid'])
File "src/obitools/_obitools.pyx", line 263, in obitools._obitools.BioSequence.__getitem__
File "src/obitools/_obitools.pyx", line 217, in obitools._obitools.BioSequence.getKey
KeyError: 'taxid'
I have also tried
obisilva --ssu --parc
where it is supposed to download the database and create the indexing files, but the progress bar stopped at 68% and didn't continue the job at all, it just stalled and it resulted in the same set of output files as mentioned above. Plus, it didn't download the fasta file, which you need later on.
Any help, would be much appreciated, thanks!
