Open nick-youngblut opened 1 year ago
nick-youngblut
commented
1 year ago While there are some instructions at https://hrgv.github.io/phyloFlash/install.html for manual setup of the database, the instructions are not detailed enough to fully set up the database.
osvatic
commented
1 year ago I just spent some time today to figure out the issue.
You can complete to installation of the database by using wget to download the proper files and adding them into the command in the link.
#wget silva DB, location found using phyloflash error log
wget https://ftp.arb-silva.de/current/Exports/SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta.gz
#wget UniVec DB, location found using phyloflash error log
wget https://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec
#use downloaded files as inputs for db.
phyloFlash_makedb.pl --CPUs 16 --silva_file SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta.gz --univec_file UniVec
The exact path the you need to use for the -db_home option will be printed out at the end of the command.
Unaimend
commented
1 year ago I get the same error on my side
nick-youngblut
commented
1 year ago adding them into the command in the link
@osvatic There are many commands at https://hrgv.github.io/phyloFlash/install.html. I'm assuming you mean:
phyloFlash_makedb.pl --univec_file /path/to/Univec --silva_file /path/to/SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz@nick-youngblut That command is the final one but it get around the issue but you need to use the wget commands (shown in previous comment and below). They will download the correct versions of the silva and UniVec databases for you to run the phyloFlash_makedb.pl command.
#wget silva DB, location found using phyloflash error log
wget https://ftp.arb-silva.de/current/Exports/SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta.gz
#wget UniVec DB, location found using phyloflash error log
wget https://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec
kbseah
commented
1 year ago Thanks for taking the time to help each other out. I've updated the docs based on the ambiguities that have been pointed out here.
Preformatted SILVA databases are now available for download from Zenodo. This will be displayed as the preferred setup method once the pull request is accepted.
Background to some of the design decisions: When phyloFlash was originally developed, SILVA was released under a license that did not allow commercial use beyond a test period, which is why the database setup script was designed to explicitly display the license conditions and get interactive user confirmation before continuing. SILVA 138 onwards is released under CC-BY 4.0, which is more permissive, but we didn't change the database setup because it still worked and active development was essentially complete.
As mentioned in https://github.com/HRGV/phyloFlash/issues/133,
phyloFlash_makedb.pl --remotefails with the following error:My conda env:
My OS: Ubuntu 20.04.5