Question: bam2cfg.pl not able to find statistics : Breakdancer
0
gravatar for sunnykevin97
12 days ago by
sunnykevin970 wrote:

HI, I followed this link Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run bam2cfg.pl It doesn't work for me, how to sort out ?.

 wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib --force
--2018-10-04 21:24:11--  http://cpanmin.us/
Resolving cpanmin.us cpanmin.us)... 151.101.130.217, 151.101.2.217, 151.101.194.217, ...
Connecting to cpanmin.us cpanmin.us)|151.101.130.217|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 302780 (296K) [text/plain]
Saving to: ‘STDOUT’

100%[==================================================================================================================================================================>] 3,02,780    --.-K/s   in 0.02s   

2018-10-04 21:24:11 (18.5 MB/s) - written to stdout [302780/302780]

--> Working on App::cpanminus
Fetching http://www.cpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz ... OK
Configuring App-cpanminus-1.7044 ... OK
Building and testing App-cpanminus-1.7044 ... FAIL
! Installing App::cpanminus failed. See /home/pinn/.cpanm/work/1538668451.38309/build.log for details. Retry with --force to force install it.
--> Working on local::lib
Fetching http://www.cpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz ... OK
Configuring local-lib-2.000024 ... OK
==> Found dependencies: ExtUtils::MakeMaker
--> Working on ExtUtils::MakeMaker
Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/ExtUtils-MakeMaker-7.34.tar.gz ... OK
Configuring ExtUtils-MakeMaker-7.34 ... OK
Building and testing ExtUtils-MakeMaker-7.34 ... FAIL
! Installing ExtUtils::MakeMaker failed. See /home/pinn/.cpanm/work/1538668451.38309/build.log for details. Retry with --force to force install it.
! Installing the dependencies failed: Installed version (6.68) of ExtUtils::MakeMaker is not in range '7.00'
! Bailing out the installation for local-lib-2.000024.
assembly gen software error • 90 views
ADD COMMENTlink modified 12 days ago by RamRS18k • written 12 days ago by sunnykevin970

Read the logs, it should have the cause of the install failure:

less /home/pinn/.cpanm/work/1538668451.38309/build.log
ADD REPLYlink written 12 days ago by h.mon20k

The bam2cfg.pl program requires three Perl modules. That has to be installed first on your system.

starting few lines of code taken from bam2cfg.pl

use strict;
use warnings;
use Getopt::Std;
use Statistics::Descriptive;
use GD::Graph::histogram;
use FindBin qw($Bin);
use lib "$FindBin::Bin";
#use lib '/gscuser/kchen/1000genomes/analysis/scripts/';
use AlnParser;

As you mentioned in your question, the error says the system is not able to find out Statistics::Descriptive module, so simply try to install it first with the help of CPAN.

sudo cpan install Statistics::Descriptive

You might get one more error while running this program, which will be concern about GD::Graph module. You need to install it too if it is not there on system.

To Resolve the GD:Graph issue you first have to install GD graph library (Tested on ubuntu 16.04 Server).

sudo apt-get install libgd2-xpm-dev
sudo cpan install GD::Graph::histogram
ADD REPLYlink modified 12 days ago • written 12 days ago by Nitin Narwade280

sudo ...

Nuh-uh, don't suggest sudo unless absolutely required (which is almost always never the case).

ADD REPLYlink written 12 days ago by RamRS18k

My general advice would be to stop using breakdancer. A whole host of more faster, more reliable, and more robust algorithms now exists (manta, lumpy, etc, etc)

ADD REPLYlink written 12 days ago by Chris Miller20k

thanks for your suggestion.

ADD REPLYlink written 11 days ago by sunnykevin970
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