Hello.
I am trying Bowtie. It seams very fast and efficient!
However I have a minor problem in my installation (windows XP)
1 - I downloaded Bowtie from the link
file: bowtie-0.9.8.1-bin-win32.zip
2 - Unzipped to C:/bowtie
3 - Test it:
bowtie -t e_coli reads/e_coli_1000.fq e_coli.map
Bowtie website says:
"This run calculates the same alignments as the previous run, but the alignments are written to e_coli.map (the final argument) rather than to the screen. Also, the -t option instructs Bowtie to print timing statistics, which will look something like this (times will obviously differ):
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Seeded quality full-index search: 00:00:01
Reported 699 alignments to 1 output stream(s)
Time searching: 00:00:01
Overall time: 00:00:01
"
However in my computer the output stops after the first two lines and stays like that forever if I let him.
Something like this:
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
When I check the file with the results (e_coli.map) it seams complete. With the 699 lines...
I am not sure if I should have done some compilation or installation of Bowtie before starting the runs. I merely downloaded it into a folder and execute the command..
Any ideas or thoughts?
Thanks!
Ines
I am trying Bowtie. It seams very fast and efficient!
However I have a minor problem in my installation (windows XP)
1 - I downloaded Bowtie from the link
file: bowtie-0.9.8.1-bin-win32.zip
2 - Unzipped to C:/bowtie
3 - Test it:
bowtie -t e_coli reads/e_coli_1000.fq e_coli.map
Bowtie website says:
"This run calculates the same alignments as the previous run, but the alignments are written to e_coli.map (the final argument) rather than to the screen. Also, the -t option instructs Bowtie to print timing statistics, which will look something like this (times will obviously differ):
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Seeded quality full-index search: 00:00:01
Reported 699 alignments to 1 output stream(s)
Time searching: 00:00:01
Overall time: 00:00:01
"
However in my computer the output stops after the first two lines and stays like that forever if I let him.
Something like this:
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
When I check the file with the results (e_coli.map) it seams complete. With the 699 lines...
I am not sure if I should have done some compilation or installation of Bowtie before starting the runs. I merely downloaded it into a folder and execute the command..Any ideas or thoughts?
Thanks!
Ines
Comment