`setup_db.pl` not finding the SILVA database

[MatteoSchiavinato]

Hi, I'm having trouble installing the database with setup_db.pl. This is likely connected with Issue #41 but I don't think it's the same, because the script I cloned from github today (May 25th, 2021) likely has fixed that issue already.

I see that the script has a hard-coded link to the current SILVA version, but this is the log I get:

[schmat90@l42 metaERG]$ /binfl/lv71579/schmat90/software/metaERG/1.2.3/bin/setup_db.pl -o /binfl/lv71579/schmat90/software/metaERG/db -v 132
[Tue May 25 15:37:36 2021] construct db directories
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/db
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/tmp
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/db\/diamond
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/db\/hmm
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/db\/sqlite3
[Tue May 25 15:37:36 2021] Running: mkdir -p \/binfl\/lv71579\/schmat90\/software\/metaERG\/db\/db\/blast
[Tue May 25 15:37:36 2021] Fetching SILVA_132_SSURef_Nr99_tax_silva_trunc.fasta.gz
Use of uninitialized value in die at /binfl/lv71579/schmat90/software/metaERG/1.2.3/bin/setup_db.pl line 761.
Died at /binfl/lv71579/schmat90/software/metaERG/1.2.3/bin/setup_db.pl line 761.

Is there a workaround?

[MatteoSchiavinato]

I solved it using 1) the workaround suggested in Issue #41 , and 2) installing File::Fetch which wasn't already installed in my case. Please add File::Fetch to the required dependencies!