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Old 04-25-2014, 08:48 AM   #1
Daniel Fernandez
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Default Bioperl error in bacterial annotation

Hi, I installed PROKKA pipeline for annotation of a bacterial genome. One of its dependencies is BioPerl, I installed this according to http://www.bioperl.org/wiki/Installing_BioPerl_on_Unix, the "preparating to install" and "installing using Built.PL" sections, never show me error, but when I run this pipeline, it show me:

Code:
[11:12:56] This is prokka 1.8
[11:12:56] Written by Torsten Seemann <torsten.seemann@monash.edu>
[11:12:56] Victorian Bioinformatics Consortium - http://www.vicbioinformatics.com
[11:12:56] Local time is Fri Apr 25 11:12:56 2014
[11:12:56] You are dnl
[11:12:56] Operating system is linux
[11:12:56] You have BioPerl 1.006001
[11:12:56] Please install BioPerl 1.006002 or higher
This is the file "prokka", the bioperl section:

Code:
# check BioPerl version 
my $minbpver = "1.006002"; # for Bio::SearcIO::hmmer3
my $bpver = $Bio::Root::Version::VERSION;
msg("You have BioPerl $bpver");
err("Please install BioPerl $minbpver or higher") if $bpver < $minbpver;
I think that not exist 1.006002 only 1.006.001,

I try to install again bioperl but it show the same. My laptop is Ubuntu 14.04, 64 bit. I installed prokka on a desktop computer (Ubuntu 12.04, 64 bits) and work very well!!!. I don't know, please help.

Thanks.
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Old 04-25-2014, 01:08 PM   #2
SES
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It looks like there was no problem with the installation, but rather there is a problem with the version you installed. How are you installing BioPerl, through CPAN or a downloaded package? The problem is that you have a very old version of BioPerl and the solution would be to update it. My recommendation would be to install the latest version (this is the default for CPAN) and try again.
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Old 06-25-2014, 08:14 AM   #3
foeckingmf
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Default have a similar issue

I have also been trying to install prokka, and in my BioPerl installation it fails. Prokka requires some modules that are not in the standard perl libraries. I installed the "XML/Simple.pm" module, but it then asked for the module "Bio/Root/Version.pm"

Command is "sudo cpan install Bio/Root/Version.pm"

resulting in:
Code:
Test Summary Report
-------------------
t/Map/Physical.t                     (Wstat: 0 Tests: 40 Failed: 0)
  TODO passed:   40
t/Seq/Seq.t                          (Wstat: 65280 Tests: 33 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 73 tests but ran 33.
t/SeqTools/SeqUtils.t                (Wstat: 65280 Tests: 43 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 133 tests but ran 43.
t/Tools/Analysis/Protein/ELM.t       (Wstat: 256 Tests: 15 Failed: 1)
  Failed test:  14
  Non-zero exit status: 1
t/Tools/Run/RemoteBlast.t            (Wstat: 512 Tests: 17 Failed: 2)
  Failed tests:  7, 17
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 21 tests but ran 17.
t/Tools/Run/RemoteBlast_rpsblast.t   (Wstat: 256 Tests: 7 Failed: 1)
  Failed test:  5
  Non-zero exit status: 1
Files=337, Tests=19150, 512 wallclock secs ( 2.18 usr  0.41 sys + 72.77 cusr  4.42 csys = 79.78 CPU)
Result: FAIL
Failed 5/337 test programs. 4/19150 subtests failed.
  CJFIELDS/BioPerl-1.6.923.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.923.tar.gz
Running Build install
  make test had returned bad status, won't install without force
I'm not sure I can manually install all of the modules this package seems to require. Has anyone successfully installed prokka, and what kind of system/libraries do you have?

Mark
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Old 06-25-2014, 08:21 AM   #4
SES
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Some of the BioPerl tests will fail, I wouldn't worry about that unless you get errors trying to load a class (that would indicate the installation was not successful). Try out prokka now and see what happens.
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Old 06-25-2014, 08:32 AM   #5
foeckingmf
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Thank you, but it returns the same error as before I tried to install the module:

Code:
Can't locate Bio/Root/Version.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /home/foeckingmf/Desktop/prokka-1.9/bin/prokka line 29.
BEGIN failed--compilation aborted at /home/foeckingmf/Desktop/prokka-1.9/bin/prokka line 29.
Mark
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Old 06-25-2014, 08:49 AM   #6
SES
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That indicates that BioPerl wasn't installed, which is clear from the test report (sorry for the quick reply or I would have seen that). Just try to install again with "force install" and it should work. I know if feels like a dirty hack, but this is the solution until the tests are fixed in the BioPerl source.
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Old 06-25-2014, 07:13 PM   #7
gaoch
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As in CPAN, the latest version of BioPerl is BioPerl-1.6.901. Install with cpan, don't use the source with ubuntu distribution.

just type: sudo cpan -i BioPerl
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Old 06-26-2014, 01:24 AM   #8
SES
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Quote:
Originally Posted by gaoch View Post
As in CPAN, the latest version of BioPerl is BioPerl-1.6.901. Install with cpan, don't use the source with ubuntu distribution.

just type: sudo cpan -i BioPerl
The latest version on CPAN is 1.6.923. See here: https://metacpan.org/pod/BioPerl

Also, that command won't fix the install as you can see above in the thread because some of the tests will fail.
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Old 06-26-2014, 03:41 AM   #9
hpm
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A quick check in Ubuntu, suggests that you would be fine with the standard Debian packages, unless you are running an old version of Ubuntu (from http://packages.ubuntu.com/trusty/bioperl):
  • Ubuntu 10.04 LTS: bioperl 1.6.1-1ubuntu1
  • Ubuntu 12.04 LTS: bioperl 1.6.901-2
  • Ubuntu 14.04 LTS: bioperl 1.6.923-1

So you could just use:

Code:
sudo apt-get install bioperl
Which would pull in all the required dependencies, including Perl modules and binary libraries, required for BioPerl.

NB. In my experience attempting to mix and match with OS package management and CPAN based Perl installation methods can cause version problems, and is best avoided if possible. So in general it is best to pick one method and stick with it, rather than trying to use both.
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Old 06-26-2014, 04:36 AM   #10
foeckingmf
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Thanks to everyone's replies - I did get it up and running although I'm not quite sure how. One of the big issues was permissions. I used the instructions from here:

http://2013-cse801.readthedocs.org/e...nnotation.html

and manually ran the make and make install commands using sudo when needed.

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