Thread Rating:
  • 0 Vote(s) - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
ecotag with custom reference library
#1
Hi,
I've built a custom reference library from in house sequencing and converted it to an ecopcr database with obiconvert. Now, I'm trying to use it to assign taxonomy to my data. I downloaded taxonomic data as a taxdumptar.gz from NCBI. I'm getting errors when I run ecotag, it seems maybe my obiconvert didn't work right, as apparently i'm missing a .pdx file?
Thanks very much in advance for help! 
Davon

Obiconvert code: obiconvert  --fasta --ecopcrdb-output=customdb -t ./TAXO ./custom/custom_ref_lib.fasta

output files:

  24328144 24 Aug 17:04 customdb.adx
146202025 24 Aug 17:04 customdb.ndx
           385 24 Aug 17:03 customdb.rdx
  75063901 24 Aug 17:03 customdb.tdx
     130312 24 Aug 17:04 customdb_001.sdx

ecotag code:
ecotag -d customdb -R ./custom/custom_ref_lib.fasta ./EKB_run1/ebl_data/ebl.fasta ebl.taxonomy.fasta

ecotag error:

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: 'customdb.pdx'
 [INFO : Preferred taxon name file not found]
 ok
Reading reference DB ...  : 750
Traceback (most recent call last):
  File "/Users/DC/Code/OBITools-1.2.10/export/bin/ecotag", line 345, in <module>
    assert seqid not in taxonlink
AssertionError
Reply


Messages In This Thread
ecotag with custom reference library - davon - 08-25-2017, 05:15 PM

Forum Jump:


Users browsing this thread: 1 Guest(s)