bowtie2 2.6.0 command not found

[cmccabe]

I downloaded bowtie2-2.6.0 from github, extracted, and installed it. I added it to path using:

 echo "export PATH=\$PATH:export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0"/" >> ~/.bashrc

and confirmed it using:

 cat ~/.bashrc

 /media/C2F8EFBFF8EFAFB9/picard-tools-1.135/:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/

it appears to be added but when I try to build and index using combined files from chromFA.tar.gz using:

 bowtie2-build hg19.fa hg19
No command 'bowtie2-build' found, did you mean:
 Command 'bowtie-build' from package 'bowtie' (universe)
bowtie2-build: command not found

What did I do wrong? Thank you .

[GenoMax]

You probably need to set the path to a directory lower than now

$ /media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/bin

[cmccabe]

I mounted the directorry to the desktop and added path again.... it recognizes bowtie2 but throws an error:

 dnascopev@ubuntu:~$ cd "/home/dnascopev/Desktop/hg19_fasta"
dnascopev@ubuntu:~/Desktop/hg19_fasta$ bowtie2-build hg19.fa hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

If I am reading the error right it can not find the hg19.fa but that file is directory (/home/dnascopev/Desktop/hg19_fasta). Any suggestions? Thanks .

[GenoMax]

When things are not in the current directory (or in $PATH) it is simple to provide the full/relative path to the file/directory in question.

$ bowtie2-build ./hg19.fa hg19 OR
$ bowtie2-build /home/dnascopev/Desktop/hg19_fasta/hg19.fa hg19

Is there a reason your are building these yourself than getting them from iGenomes?

[cmccabe]

I tried both:

dnascopev@ubuntu:~/Desktop/hg19_fasta$ bowtie2-build /home/dnascopev/Desktop/hg19_fasta/hg19.fa hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory
dnascopev@ubuntu:~/Desktop/hg19_fasta$ bowtie2-build ./hg19.fa hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

I am downloaded from iGenomes, just curious why its not working.

.bashrc

export PATH=$PATH:/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0

Thanks .

[GenoMax]

Have you tried

$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa hg19

Is that file actually present?

$ ls -lh /home/dnascopev/Desktop/hg19_fasta/*.fa

These indexes should already be present in Sequences/Bowtie2Index directory (base name genome), if you had downloaded the bundle from iGenomes.

[cmccabe]

 dnascopev@ubuntu:~$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

The fie appears to be there.

 dnascopev@ubuntu:~$ ls -lh /home/dnascopev/Desktop/hg19_fasta/*.fa
-rw-rw-r-- 1 dnascopev dnascopev 3.0G Jun 22 10:17 /home/dnascopev/Desktop/hg19_fasta/hg19.fa

[GenoMax]

You do have write permissions in that directory?

$ touch /home/dnascopev/Desktop/hg19_fasta/test
$ ls -l /home/dnascopev/Desktop/hg19_fasta/test

[cmccabe]

The permissions on that directory are set to create and delete

 dnascopev@ubuntu:~$ touch /home/dnascopev/Desktop/hg19_fasta/test
dnascopev@ubuntu:~$ ls -l /home/dnascopev/Desktop/hg19_fasta/test
-rw-rw-r-- 1 dnascopev dnascopev 0 Aug 10 13:10 /home/dnascopev/Desktop/hg19_fasta/test

a file test was created that was 0 bytes. Thank you.

[GenoMax]

Did you compile bowtie2 package yourself or download a pre-compiled version?

One last try

$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19

[cmccabe]

 dnascopev@ubuntu:~$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

I downloaded the package from github, extracted, and added the directory to path where bowtie2 is.

 export PATH=$PATH:/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0

I also made it executable using:

 chmod +x /home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2*

as I was getting an error:

 No command 'bowtie2-build' found, did you mean:
 Command 'bowtie-build' from package 'bowtie' (universe)
bowtie2-build: command not found

making bowtie2 executable fixed one issue but lead to another. Thank you .

[GenoMax]

Wow .. my head is starting to hurt

Why did you put the bowtie2 executables under the directory with the fasta sequence? There is no logical explanation as to why this is not working .. perhaps bowtie does not like to have any other files/directories where it is working.

If you are willing .. try the following (I am assuming that the executable files are right in bowtie2-2.6.0 directory):

$ mv /home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0 /home/dnascopev/Desktop/
$ export PATH=$PATH:/home/dnascopev/Desktop/bowtie2-2.6.0
$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19

[cmccabe]

 dnascopev@ubuntu:~$ mv /home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0 /home/dnascopev/Desktop/
dnascopev@ubuntu:~$ export PATH=$PATH:/home/dnascopev/Desktop/bowtie2-2.6.0
dnascopev@ubuntu:~$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

downloaded the zip from: https://github.com/BenLangmead/bowtie2 as I am blocked from sourceforge.

Thank you for all your help .

[GenoMax]

I compiled v.2.2.6 from GitHub and can build indexes without any problem so the source files on GitHub are fine.

How about

$ ls -lh /home/dnascopev/Desktop/bowtie2-2.6.0/bowtie*

[cmccabe]

I am going to re-install. Did you have to do anything besides download, extract, and add to path? Was chmod or make necessary? Thank you