Entering edit mode
7.1 years ago
benkirk86
•
0
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
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 (changepath_to
part to actual value on your machine).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.
Do you see a listing when you do
ls -lh e_coli reads/e_coli_1000.fq
from that directory?No it is not listed
is what it returns.
I've already changed my bash_profile. I am lost on what to do.
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.
Thanks for the link! And your help. The argument is tripping me up, I will get it figured out