Hello there and thank you for your welcome!
I have to format RDP 16S bacterial database in fasta format (downladed from here:http://rdp.cme.msu.edu/misc/resources.jsp) to fit in a BLAST search, carried out with QIIME command 'assign_taxonomy.py'.
I need to create an index from the fasta file and I have read that this can be done by using 'formatdb' in the BLAST standsalone program, but when I try to do it I always get a message like this one:
[formatdb 2.2.22] ERROR: RDP_11_2_index.txt.nhrOutput
Blast-def-line-set.E.<title>
Invalid value(s) [9] in VisibleString [uncultured bacterium; DolOr_72351#Lineage=Root;rootrank;Bacteria;domain;unclassified_Bacteria; ...]
However, I get a .nhr file, but with data in this shape:
S000655540¢Ä0Ä0ĆÄňuncultured actinobacterium; GASP-KA1W3_B01#Lineage=Root;rootrank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Ilumatobacter;genus°Ä0ĆİÄ
With unknown characters that does not allow to use it with BLAST option or in any other BLAST search.
Could any one help me with this issue? I am really stuck at this step...
Thanks a lot
MA
I have to format RDP 16S bacterial database in fasta format (downladed from here:http://rdp.cme.msu.edu/misc/resources.jsp) to fit in a BLAST search, carried out with QIIME command 'assign_taxonomy.py'.
I need to create an index from the fasta file and I have read that this can be done by using 'formatdb' in the BLAST standsalone program, but when I try to do it I always get a message like this one:
[formatdb 2.2.22] ERROR: RDP_11_2_index.txt.nhrOutput
Blast-def-line-set.E.<title>
Invalid value(s) [9] in VisibleString [uncultured bacterium; DolOr_72351#Lineage=Root;rootrank;Bacteria;domain;unclassified_Bacteria; ...]
However, I get a .nhr file, but with data in this shape:
S000655540¢Ä0Ä0ĆÄňuncultured actinobacterium; GASP-KA1W3_B01#Lineage=Root;rootrank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Ilumatobacter;genus°Ä0ĆİÄ
With unknown characters that does not allow to use it with BLAST option or in any other BLAST search.
Could any one help me with this issue? I am really stuck at this step...
Thanks a lot
MA
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