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!
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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
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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.
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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
bowtie2-build ./sequence.fa myseqLast edited by GenoMax; 10-07-2013, 12:05 PM.
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Bowtie2 Error
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!Tags: None
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