Trouble with ecoPCR/ecotag
Hello, After following your instructions on the wolf diet webpage, I keep having issues with generating a database from the EMBL sequences. I can get obiconvert to process the files but it seems it is not generating the .pdx file. This seems to cause problems for taxon assignment. Here are the commands and error. Any help would be appreciated.
ecotag -d embl_last -R db_v05_r117.fasta VM061719-001.ali.assigned.uniq.c10.l80.fasta > VM061719-001.ali.assigned.uniq.c10.l80.tag.fasta Reading binary taxonomy database... [INFO : Taxon alias file found] [INFO : Local taxon file not found] Taxonomical tree read [Errno 2] No such file or directory: 'embl_last.pdx' [INFO : Preferred taxon name file not found] ok Reading reference DB ... [Errno 2] No such file or directory: 'db_v05_r117.fasta' (base) matt_hopken@abdoserver1:~/Vector_metagenomics/PR_bloodmeal$ obigrep -d embl_last --require-rank=species --require-rank=genus --require-rank=family 12sV5.ecopcr > 12sV5_clean.fasta Reading binary taxonomy database... [INFO : Taxon alias file found] [INFO : Local taxon file not found] Taxonomical tree read [Errno 2] No such file or directory: 'embl_last.pdx' [INFO : Preferred taxon name file not found] ok 12sV5.ecopcr 100.0 % |##################################################/] remain : 00:00:00
Thank you!