Bowtie2 Warnings after make command and errors after trying to use bowtie2-build
1
0
Entering edit mode
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__
errread, errwrite)
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
ADD COMMENT
2
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?

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 1526 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6