Rookie question-running Bowtie from Terminal

Question

[benkirk86]

Hi, I am running into trouble on the first line of the Bowtie tutorial. This question has been asked before but I haven't found an answer to it. I am absolutely in the correct directory. Can anybody help with how to fix this? Thanks!

When i enter >>

./bowtie e_coli reads/e_coli_1000.fq

this gets returned:

Traceback (most recent call last): File "./bowtie", line 91, in <module> main() File "./bowtie", line 88, in main os.execv(bin_spec, bowtie_args) OSError: [Errno 2] No such file or directory

[GenoMax]

The path (relative) that you are providing does not appear to be correct (e_coli reads/e_coli_1000.fq). You could provide the full path /path_to/e_coli reads/e_coli_1000.fq and see if that helps (change path_to part to actual value on your machine).

[benkirk86]

From webpage tutorial: "The Bowtie source and binary packages come with a pre-built index of the E. coli genome, and a set of 1,000 35-bp reads simulated from that genome. To use Bowtie to align those reads, issue the following command. If you get an error message "command not found", try adding a ./ before the bowtie.

bowtie e_coli reads/e_coli_1000.fq

The first argument to bowtie is the basename of the index for the genome to be searched. The second argument is the name of a FASTQ file containing the reads."

Yeah, my pwd is ~/bowtie-1.2 where the folder is located.

[GenoMax]

Do you see a listing when you do ls -lh e_coli reads/e_coli_1000.fq from that directory?

[benkirk86]

No it is not listed

ls -lh e_coli reads/e_coli_1000.fq
ls: e_coli: No such file or directory
-rw-r--r--@ 1 benkirk86  staff    78K Dec 19 22:29 reads/e_coli_1000.fq

is what it returns.

I've already changed my bash_profile. I am lost on what to do.

[GenoMax]

What you are trying to do is run bowtie with pre-made index for e_coli genome. Those index files are in a separate directory called indexes. So your command needs to be

./bowtie indexes/e_coli reads/e_coli_1000.fq

You may want to spend a couple of hours at this site to familiarize yourself with basics of unix. It will make things much clearer.

[benkirk86]

Thanks for the link! And your help. The argument is tripping me up, I will get it figured out