nodesdb not generated

[ccgallen]

Hi! I am using blobtools 1.1.1 installed with miniconda. I followed the instructions to install the nodesdb and no file is generated using blobtools nodesdb. Any idea what I am doing wrong?

Thanks,
Carmen

(base) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -P data/
--2021-03-19 18:41:02-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
=> ‘data/taxdump.tar.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.229, 165.112.9.228, 2607:f220:41e:250::13, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.229|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /pub/taxonomy ... done.
==> SIZE taxdump.tar.gz ... 54735134
==> PASV ... done. ==> RETR taxdump.tar.gz ... done.
Length: 54735134 (52M) (unauthoritative)

taxdump.tar.gz 100%[=============================================================>] 52.20M 29.6MB/s in 1.8s

2021-03-19 18:41:06 (29.6 MB/s) - ‘data/taxdump.tar.gz’ saved [54735134]

(base) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ tar zxf data/taxdump.tar.gz -C data/ nodes.dmp names.dmp
(base) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ ls
data
(base) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ ls data
names.dmp nodes.dmp taxdump.tar.gz
(base) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ conda activate blobtools-env
(blobtools-env) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ blobtools nodesdb --nodes data/nodes.dmp --names data/names.dmp
[+] Creating nodesDB from data/nodes.dmp and data/names.dmp
(blobtools-env) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ ls
data
(blobtools-env) ccallen@debary-vm1:/data/databases/blobtools_nodesdb$ blobtools -v
1.1.1

[AntoineHo]

Hello,

I had a similar issue, after looking at the code, the database is actually written somewhere in the miniconda environment. In my case it was written at: /home/user/env/blobtools/lib/python3.6/site-packages/data/nodesDB.txt

Maybe try using something like: find /home/user/env/blobtools | grep "nodesDB.txt" to get the path in your system.

Cheers,
Antoine

[ccgallen]

OK I will check thanks!!