ERROR: Bio::Perl not installed

[Cindy0805]

Hi, I am very new in using Docker, sorry if I am bothering your with my stupid questions. I have followed your instruction to pull the image from docker hub using: $ docker pull nextgenusfs/funannotate then I did $ wget -O funannotate-docker https://raw.githubusercontent.com/nextgenusfs/funannotate/master/funannotate-docker $ chmod +x /path/to/funannotate-docker

I managed to run the command: $ funannotate-docker test -t predict --cpus 12 However, when I run $ funannotate-docker check it shows me that ERROR: Bio::Perl not installed, install with cpanm Bio::Perl

Is is because the Bio::Perl is missing in the dockerfile or do I need to solve it differently?

My another stupid question is how do I link external dependencies to the docker? thanks!

Cheers Xiaoqian

[nextgenusfs]

That should be a harmless warning -- BioPerl isn't required in latest release but it seems I forgot to take it off the list for the check function. Thanks.

What sort of external dependencies do you want to link too? Connecting docker containers is possible although it can be a challenge, docker-compose is one tool that can link containers together. I generally provide the docker container as an easy entry for users to give it a try -- it would function better in an HPC ecosystem with a more manual/conda installation so that other tools that do not fit in the docker container can be utilized.

[Cindy0805]

thanks for your reply!

sorry for not specifying my question. I got errors about several external dependencies, so I am wondering if I need to mount/link those. Please see the error below (although I have added "GENEMARK_PATH=/media/xiaoqian/data1/bin/gm_et_linux_64" in the bash wrapper script that you have provided):

ImportError: cannot import name 'TextFace' from 'ete3' (/venv/lib/python3.8/site-packages/ete3/init.py) ERROR: emapper.py not installed ERROR: ete3 not installed ERROR: gmes_petap.pl not installed ERROR: signalp not installed

Thanks a lot for providing the docker option for HPC, this is exactly what I need. I am testing running so later I can run with a genome on HPC.

I tried "funannotate train", however I got error relating PASA: DBD::SQLite::db prepare failed: database is locked at /venv/opt/pasa-2.4.1/PerlLib/DB_connect.pm line 160. Error DBD::SQLite::db prepare failed: database is locked at /venv/opt/pasa-2.4.1/PerlLib/DB_connect.pm line 160. at /venv/opt/pasa-2.4.1/PerlLib/DB_connect.pm line 162. DB_connect::do_sql_2D(DB_connect=HASH(0x556ff6bb3448), "select al.align_id, al.align_acc from subcluster_link sl, ali"..., 2019) called at /venv/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms_per_subcluster.dbi line 63

Could you help me with solving this issue? I am not sure if this is because of the docker container or I am supposed to link/change anything locally to run it correctly.

thanks a lot in advance.

Cheers

[estolle]

I have the same error about bioperl "ERROR: Bio::Perl not installed, install with cpanm Bio::Perl"

I installed Funannotate via conda (current version, v1.8.9) I then tried to install Bioperl manually inside the conda env, but it fails with the following errors related to Bio::DB::GenBank

building and testing Bio-DB-NCBIHelper-1.7.7 ... FAIL ! Installing Bio::DB::GenPept failed. See /root/.cpanm/work/1633943610.67054/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'Bio::DB::GenPept' is not installed, Module 'Bio::DB::GenBank' is not installed

the logfile has errors related to testing the remote connection or something:

MSG: WebDBSeqI Request Error: 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (Temporary failure in name resolution) and therefore two of its internal tests fail.

ATM not sure how to fix this.

Best Eckart

[estolle]

The BioPerl error can be fixed like this (at least in the conda env):

activate the funannotate environment

cpanm --force Bio::DB::GenBank
cpanm Bio::Perl

[philgoetz]

I have the same error about bioperl "ERROR: Bio::Perl not installed, install with cpanm Bio::Perl"

I installed Funannotate via conda (current version, v1.8.9) I then tried to install Bioperl manually inside the conda env, but it fails with the following errors related to Bio::DB::GenBank

building and testing Bio-DB-NCBIHelper-1.7.7 ... FAIL ! Installing Bio::DB::GenPept failed. See /root/.cpanm/work/1633943610.67054/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'Bio::DB::GenPept' is not installed, Module 'Bio::DB::GenBank' is not installed

the logfile has errors related to testing the remote connection or something:

MSG: WebDBSeqI Request Error: 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (Temporary failure in name resolution) and therefore two of its internal tests fail.

ATM not sure how to fix this.

Best Eckart

There are 2 problems installing Bio-DB-NCBIHelper-1.7.7 .

1. NCBI's servers go down ALL THE TIME. I think they're down more-often than they're up.

2. Many of the tests for Bio-DB-NCBIHelper-1.7.7 are obsolete. They check various downloaded data against the values it had when the tests were written. But that sequence data is being constantly updated. For instance, the phylum Actinomycetia has been renamed Actinomycetes.

Like estolle said, use of --force is helpful here.