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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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nodesdb not generated #115

Open ccgallen opened 3 years ago

ccgallen commented 3 years ago

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 commented 2 years ago

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 commented 2 years ago

OK I will check thanks!!