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  • #62

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Opened Mar 14, 2021 by saeed mohamadzade@saeedmn2005

Problem in making database for metabarcoding analysis

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.

Edited Mar 14, 2021 by saeed mohamadzade
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Reference: obitools/obitools#62