Bowtie2 Warnings after make command and errors after trying to use bowtie2-build
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20 months ago
guto03 ▴ 10

I've been trying to run bowtie2 with no success.

At first, I tried to run make in the bowtie2 source folder. But then I got lots of warnings saying this and this package are deprecated.

I thought it could be okay still and then proceeded to trying to follow the tutorial from bowtie's website in order to run the example with the lambda phage.

I got this error after trying to run the command ../bowtie2-master/bowtie2-build ./bowtie2-master/example/reference/lambda_virus.fa lambda_virus:

File "../bowtie2-master/bowtie2-build", line 90, in <module>
main()
File "../bowtie2-master/bowtie2-build", line 87, in main
sys.exit(subprocess.call(list(argv)))
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 172, in call
return Popen(*popenargs, **kwargs).wait()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 394, in __init__
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory


My present directory was: /Users/ltelles/Desktop/documents_desktop/bioinformatics/bowtie2_example_project

I already tried to export the directory to the PATH variable and tried to set the variable BT2_HOME pointing to the source folder. Neither worked and I got this:

zsh: no such file or directory: /User/ltelles/Desktop/documents_desktop/bioinformatics/bowtie2-master/bowtie2-build


I am sure the bowtie2-build file is there, I checked.

What is going on and why can't I use it?

alignment bowtie2 python • 621 views
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Entering edit mode
20 months ago
GenoMax 108k

Which OS are you doing this on? Why not just use the pre-compiled binaries (if you are using linux/macOS) that are available from there?

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I'm using MacOS Catalina. When I unzip this pre-compiled binary it is extracted as bowtie 1.2.3 and not bowtie2. The examples I ran above were obtained with bowtie2 that I downloaded from their GitHub page.

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Man, I only noticed the other files below later and there's this one specific for MacOS. I tried it and it worked the first time! Thank you so much! I was trying it the whole day without success!