Question: Bowtie2-build cannot build an index
0
gravatar for Gary
15 months ago by
Gary440
Taiwan/Taichung/China Medical University Hospital
Gary440 wrote:

I use bowtie2-build to build an index for the chicken galGal5 reference genome, but it showed error message below. The chicken galGal5 genome was downloaded from UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.fa.gz). The bowtie2 for Mac was downloaded from sourceforge (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.0/bowtie2-2.3.0-macos-x86_64.zip/download). After unzipping, I moved the folder to /Users/gary/Applications/bowtie2-2.3.0, and added a path in .bash_profile (export PATH=$PATH:/Users/gary/Applications/bowtie2-2.3.0). Could you help me? Many thanks.

gary > pwd
/Users/gary/Downloads
gary > ll
total 2451904
-rw-r--r--@ 1 gary  staff   1.2G Feb  4 01:15 galGal5.fa
gary > bowtie2-build galGal5.fa galGal5
dyld: Library not loaded: /usr/local/opt/tbb/lib/libtbb.dylib
  Referenced from: /Users/gary/Applications/bowtie2-2.3.0/bowtie2-build-s
  Reason: image not found
Trace/BPT trap: 5
index bowtie2 • 1.5k views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 15 months ago by Gary440
1

You need "thread building blocks", apparently, which is a free download.

ADD REPLYlink written 15 months ago by Devon Ryan80k

Thanks you so much. It seems working now. However, when I install "thread building blocks" using command line: brew install tbb. It showed Caveats below. Should I run the two command lines it suggested? Many thanks.

==> Downloading https://homebrew.bintray.com/bottles/tbb-4.4-20161128.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring tbb-4.4-20161128.yosemite.bottle.tar.gz

==> Caveats

Python modules have been installed and Homebrew's site-packages is not
in your Python sys.path, so you will not be able to import the modules
this formula installed. If you plan to develop with these modules,
please run:

  mkdir -p /Users/gary/.local/lib/python2.7/site-packages

  echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> /Users/gary/.local/lib/python2.7/site-packages/homebrew.pth

==> Summary

đŸș  /usr/local/Cellar/tbb/4.4-20161128: 119 files, 1.9M

gary >

ADD REPLYlink modified 15 months ago by genomax49k • written 15 months ago by Gary440
1

You're not a developer, so I wouldn't worry about it.

ADD REPLYlink written 15 months ago by Devon Ryan80k
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