Entering edit mode
3.1 years ago
saeedmn2005
•
0
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:
saeedmn@saeed-MN:~/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) saeedmn@saeed-MN:~/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.