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

wget ftp://ftp.ncbi.nlm.nih.gov/genbank/gbpln*seq.gz

and downloaded the taxonomy from NCBI using

wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 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  taxdmp_2021-03-01.zip

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/sequence.py", line 180, in __del__
    self.close()
  File "/usr/lib/python3/dist-packages/obitools/ecopcr/sequence.py", line 149, in close
    self._file.seek(0,0)
AttributeError: 'EcoPCRDBSequenceWriter' object has no attribute '_file'

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

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modified 30 minutes ago

written
2 hours ago
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saeedmn20050



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