Bowtie2 Error

[ndrakos]

Hello, I was given some fastq files and a reference genome (fasta file), and told to assemble a genome.

I managed to install bowtie2 (I have windows, and am using a cygwin terminal).

I tried to build the reference genome, but keep getting an error.

I typed:
bowtie2-build sequence.fa myseq

And the error message I receive is:

Settings:
Output files: "myseq.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
sequence.fa
Error: could not open sequence.fa
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build sequence.fa myseq


Does anyone have an idea of why I am getting this error?

Thank you for your help!

[GenoMax]

With bowtie2 you are not going to "assemble" the genome but "align" your reads to the reference genome.

Here is the relevant bit of information in your output.

Error: could not open sequence.fa

If the sequence.fa file is in the directory where you are executing bowtie2-build from then try the following:

bowtie2-build ./sequence.fa myseq

If you have not used UNIX before then perhaps spending some time at this link would help: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1

[ndrakos]

Thank you for your reply. I tried your suggestion, but got the same error (I am in the same directory).

Error: could not open ./sequence.fa

And, yes I am new to UNIX. Thank you for the link, I will look through it.

[GenoMax]

A better option would be to change to the directory where the "sequence.fa" file is located and then run the command as follows:

$/full_path_to/bowtie2-build ./sequence.fa myseq

Replace "full_path_to" with the real file path on your system.

[dpryan]

If you type:

ls

is "sequence.fa" (or whatever it's really called) one of the files listed? If not, you're in the wrong directory, which I suspect is the case.

[ndrakos]

Hi, I figured it out. I was in the right directory. The problem was that I put '.fa' instead of '.fasta'. I thought I had tried that first, but apparently not.

Thanks for your help!