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This queue is for tickets about the Bio-SamTools CPAN distribution.

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Id: 106384
Status: open
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: pgajer [...] gmail.com
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Subject: Bio-SamTools run error
Date: Wed, 12 Aug 2015 05:11:52 -0400
To: bug-Bio-SamTools [...] rt.cpan.org
From: Pawel G <pgajer [...] gmail.com>
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Hi, I have installed Bio-SamTools on my mac 10.10.4 using cpan[1]> install LDS/Bio-SamTools-1.41.tar.gz I had to point to bam.h and compiled libbam.a files "Please enter the location of the bam.h and compiled libbam.a files: /Users/pgajer/devel/packages/samtools-0.1.19" When running a simple perl script that uses Bio::DB::Sam I am getting the following error Can't load '/Library/Perl/5.18/darwin-thread-multi-2level/auto/Bio/DB/Sam/Sam.bundle' for module Bio::DB::Sam: dlopen(/Library/Perl/5.18/darwin-thread-multi-2level/auto/Bio/DB/Sam/Sam.bundle, 1): Symbol not found: _bam_nt16_rev_table Referenced from: /Library/Perl/5.18/darwin-thread-multi-2level/auto/Bio/DB/Sam/Sam.bundle Expected in: flat namespace in /Library/Perl/5.18/darwin-thread-multi-2level/auto/Bio/DB/Sam/Sam.bundle at /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194. at /Users/pgajer/projects/16S_rRNA_pipeline/perl/read_mapper.pl line 47. Line 47 of my script is use Bio::DB::Sam; I have also installed Bio-SamTools (version 1.41) from the source code, and I am still getting exactly the same error. I would very much appreciate your help with this issue Best, :) pawel
From: dan.bolser [...] gmail.com
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What version of SAMtools do you have installed? AFAIK, newer versions of SAMtools are not compatible with Bio::DB::Sam


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