Fail installation (setup stage)

[hyyuu]

Hello , thank you for the software ! But I keep failing to install the program, it always stuck at the setup stage. Full installation output as below,

(base) ada@node_b:~/0hiuyan/tools/DB_File-1.827$ fdog.setup -o /home/ada/0hiuyan/tools/fdog --conda                                                                                                                                          | tee log.txt
Current OS system: Linux
Data output path: /home/ada/0hiuyan/tools/fdog
-------------------------------------
Checking .bash_profile/.bashrc, grep, sed/gsed and wget availability...
done!
-------------------------------------
Installing dependencies...
done!
-------------------------------------
Preparing folders...
done!
-------------------------------------
Downloading and installing annotation tools/databases:
--2022-07-15 22:04:26--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
           => ‘taxdump.tar.gz’
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 165.112.9.230, 130.14.250.10, 2607:f220:41f:250::22                                                                                                                                         9, ...
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|165.112.9.230|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.
==> SIZE taxdump.tar.gz ... 58541292
==> PASV ... done.    ==> RETR taxdump.tar.gz ... done.
Length: 58541292 (56M) (unauthoritative)

taxdump.tar.gz           100%[==================================>]  55.83M  2.36MB/s    in 24s

2022-07-15 22:04:55 (2.29 MB/s) - ‘taxdump.tar.gz’ saved [58541292]

citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
gc.prt
readme.txt
Taxonomy database indexing. It can take a while, please wait...

------------- EXCEPTION -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/ada/anaconda3/lib/perl5/5.                                                                                                                                         32/core_perl/auto/DB_File/DB_File.so' for module DB_File: /home/ada/anaconda3/lib/perl5/5.32/core_pe                                                                                                                                         rl/auto/DB_File/DB_File.so: undefined symbol: db_create at /home/ada/anaconda3/lib/perl5/core_perl/X                                                                                                                                         SLoader.pm line 93.
 at /home/ada/anaconda3/lib/perl5/5.32/core_perl/DB_File.pm line 258.
Compilation failed in require at /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy/flatfile.pm                                                                                                                                          line 88.
BEGIN failed--compilation aborted at /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy/flatfil                                                                                                                                         e.pm line 88.
Compilation failed in require at /home/ada/anaconda3/lib/perl5/site_perl/Bio/Root/Root.pm line 520.

STACK Bio::Root::Root::_load_module /home/ada/anaconda3/lib/perl5/site_perl/Bio/Root/Root.pm:522
STACK (eval) /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm:295
STACK Bio::DB::Taxonomy::_load_tax_module /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm                                                                                                                                         :295
STACK Bio::DB::Taxonomy::new /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm:119
STACK toplevel /home/ada/.local/lib/python3.9/site-packages/fdog/setup/indexTaxonomy.pl:6
-------------------------------------

Bio::DB::Taxonomy: flatfile cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/ada/anaconda3/lib/perl5/5.                                                                                                                                         32/core_perl/auto/DB_File/DB_File.so' for module DB_File: /home/ada/anaconda3/lib/perl5/5.32/core_pe                                                                                                                                         rl/auto/DB_File/DB_File.so: undefined symbol: db_create at /home/ada/anaconda3/lib/perl5/core_perl/X                                                                                                                                         SLoader.pm line 93.
 at /home/ada/anaconda3/lib/perl5/5.32/core_perl/DB_File.pm line 258.
Compilation failed in require at /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy/flatfile.pm                                                                                                                                          line 88.
BEGIN failed--compilation aborted at /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy/flatfil                                                                                                                                         e.pm line 88.
Compilation failed in require at /home/ada/anaconda3/lib/perl5/site_perl/Bio/Root/Root.pm line 520.

STACK Bio::Root::Root::_load_module /home/ada/anaconda3/lib/perl5/site_perl/Bio/Root/Root.pm:522
STACK (eval) /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm:295
STACK Bio::DB::Taxonomy::_load_tax_module /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm                                                                                                                                         :295
STACK Bio::DB::Taxonomy::new /home/ada/anaconda3/lib/perl5/site_perl/Bio/DB/Taxonomy.pm:119
STACK toplevel /home/ada/.local/lib/python3.9/site-packages/fdog/setup/indexTaxonomy.pl:6
-------------------------------------


For more information about the Bio::DB::Taxonomy system please see
the Bio::DB::Taxonomy docs.  This includes ways of checking for
formats at compile time, not run time.
Can't call method "get_taxon" on an undefined value at /home/ada/.local/lib/python3.9/site-packages/                                                                                                                                         fdog/setup/indexTaxonomy.pl line 12.
Error while indexing NCBI taxonomy database! Please check /home/ada/.local/lib/python3.9/site-packag                                                                                                                                         es/fdog/taxonomy/ folder and run this setup again!

There are only three files in the /home/ada/.local/lib/python3.9/site-packages/fdog/taxonomy/
names.dmp nodes.dmp taxdump.tar.gz

Could you please suggest how to solve this error ?
Thank you very much !

[trvinh]

Hi @hyyuu ,
the problem here is that the Bioperl module Bio::DB::Taxonomy::flatfile cannot be loaded. I suppose that it was not installed, or couldn't be installed correctly. It normally happens when there is any conflict in the perl setting (e.g. the perl version from the anaconda vs the perl version from the OS, and how they are activated within the Conda env). Unfortunately, I cannot give you a fixed solution, because that issue differs from computer to computer.
Please try to install that Bioperl module manually in the Conda environment where you installed fFOG, and make sure that it can be loaded. Then you can rerun the fdog.setup command.
Please let us know if it works! Many thanks!
Best,
Vinh

[trvinh]

solved with PR #26