gravatar for saeedmn2005

2 hours ago by

Hi all,

I'm new to the OBITools and I'm trying to make database for rbcL (Chloroplast) gene. I've downloaded all plants genome using


and downloaded the taxonomy from NCBI using

wget and tar -zxvf taxdump.tar.gz

here is the result:

[email protected]:~/nesteco/TOXO$ ls
citations.dmp  division.dmp  gencode.dmp  names.dmp  readme.txt
delnodes.dmp   gc.prt        merged.dmp   nodes.dmp

When I try to convert using

obiconvert --genbank -t ../TAXO --ecopcrdb-output=ncbi_last ../NCBI/*.seq.gz

I faced the following error:

(base) [email protected]:~/nesteco/TOXO$ obiconvert --genbank -t ../TAXO --ecopcrdb-output=rbcl_last ../NCBI/*.seq.gz
[Errno 2] No such file or directory: '../TAXO/nodes.dmp'
Exception ignored in: <function EcoPCRDBSequenceWriter.__del__ at 0x7f2e2f489310>
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/obitools/ecopcr/", line 180, in __del__
  File "/usr/lib/python3/dist-packages/obitools/ecopcr/", line 149, in close,0)
AttributeError: 'EcoPCRDBSequenceWriter' object has no attribute '_file'

Can anyone suggest how I can overcome this error? Thanks in advance.


modified 30 minutes ago

2 hours ago


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