Question

Issue with installing bowtie2

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7.2 years ago

seta ★ 1.9k

Hi all,

I've downloaded the latest version of bowtie2 (bowtie2-2.3.0-linux-x86_64.zip) and try to run it on my personal account on the cluster. Based on manual, I unzipped the file, changed directory to the bowtie2 folder and type "bowtie2", which the error says: "command not found". I tried with "./bowtie2", which the below error appeared.

/gfs-dist/seta/software/bowtie2-2.3.0/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open     shared object file: No such file or directory
(ERR): Description of arguments failed!
Exiting now ...

Could you please help me what is the problem and how to solve it?

Thank you

bowtie2 installing error • 11k views

ADD COMMENT • link updated 6.5 years ago by Karma ▴ 310 • written 7.2 years ago by seta ★ 1.9k

score 2 · Answer 1 · 2017-10-13

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6.5 years ago

Karma ▴ 310

Try the following commands

sudo apt-get install libtbb-dev
sudo apt-get install g++
make

ADD COMMENT • link 6.5 years ago by Karma ▴ 310

score 1 · Answer 2 · 2017-01-31

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7.2 years ago

j_susat ▴ 40

I had the same error just a few minutes ago. In the newest Version Bowtie2 seems to need the TBB Library for better perfomance but it is missing on your cluster. However there is a way to compile it without the need of the TBB Library as stated here: Bowtie Homepage

However if you want to use Bowtie2 with TBB I would recommend to get in contact with your admin and ask him if he could set up the missing library.

ADD COMMENT • link 7.2 years ago by j_susat ▴ 40

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Thank you very much. As the link said "TBB to give superior thread scaling", could you please let me know if the speed of Bowtie without TBB library is low? However, the output of command "locate tbb" is /usr/include/freetype2/freetype/ftbbox.h , so it seems to be installed, yes?

Thanks

ADD REPLY • link 7.2 years ago by seta ★ 1.9k

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I guess you could download the Bowtie2 source code and then change the makefile so that it points to your location of the TBB library. But at the moment I'am not sure what to change.

And by the way even without the TBB library Bowtie2 is a very fast aligner. But it always depends on what you are going to do. For small mappings that will not contain millions of reads it will make no difference since you will not recognize a gain in speed.

ADD REPLY • link 7.2 years ago by j_susat ▴ 40

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Hi seta,

Just curious, is Bowtie2 faster than BBMap for this data?

ADD REPLY • link 7.2 years ago by Brian Bushnell 20k

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Hi Brian,

Unfortunately, I didn't compare the speeds of Bowtie2 and BBMap. Here, I need Bowtie2 for running tophat.

ADD REPLY • link 7.2 years ago by seta ★ 1.9k

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Don't use TopHat unless there is a pressing need. Even TopHat developers ask users to use HISAT2, successor of TopHat.

ADD REPLY • link 7.2 years ago by GenoMax 141k

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Thank you for your advice. No pressing. I just map reads on the genome (barley) for finding differentially expressed genes and some alternative splicing events. However, the HISAT2 manual says "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome)", it means the program isn't appropriate for other genomes!? I'm working on barley (plant)

Could you please kindly tell me your idea about STAR especially when compared to HISAT2?