Bowtie "could not open read file"

[AVincent]

Hi everyone,

I am new to this forum and not at all familiar with bioinformatics.
I am just starting to learn how to use Bowtie to make alignments from solexa next gen sequencing fastq files.

Here is how I ran it:

bowtie hg18 reads/Pool7_BC1_read1 Pool7_BC1_read1_output.txt

But I got this error message:

"Warning: Could not open read file "reads/Pool7_BC1_read1" for reading; skipping...
Command: bowtie hg18 reads/Pool7_BC1_read1 Pool7_BC1_read1_output.txt"

My files, such as "Pool7_BC1_read1", are FASTQ but don't have an extension. Is that the reason why Bowtie can't read them? I tried to add an extension but it didn't work either though.

I guess I am doing something wrong but I can't figure out what it is.

Thanks very much for your help,
AV

[Bardj]

You wrote:

bowtie hg18 reads/Pool7_BC1_read1 Pool7_BC1_read1_output.txt

Is that the exact command that you put in? I feel like the error message and the input you posted aren't matching up with what I would have expected.

[sp_wade]

Hi,AVincent!

There is a blank space both in your file name and path.
While in the linux OS ,the character could not be recognized.
You may rename the path and read file!

Good luck!

[AVincent]

Hi everyone,

Yes this is the exact command I wrote.

I am running Windows XP Professional x64 Edition so I used the System32\cmd.exe to try to run Bowtie and it worked for the tutorial:

http://bowtie-bio.sourceforge.net/tutorial.shtml

But when I try to input my own file, I get the error message I previoulsy mentionned...

I also tried to use MSYS as recommanded in the Bowtie manual but I can't make it work either.

Thank you very much for your help,
AV

[schmima]

hm - try:
bowtie hg18 -q reads/Pool7_BC1_read1 Pool7_BC1_read1_output.txt
(add the -q option - even though default - one never knows ^^)
but strange, that the tutorial is working... How is it with the '/' character in windows?

otherwise:
check format (?)
check permissions (?)

good luck

[AVincent]

Thanks schmima for your quick reply.

I tried to add the -q option but got the same warning...
The format is FASTQ.
Can I ask you what you mean by "check permission"?

Thanks!

[schmima]

to check the file permission - so if bowtie is allowed to open it (don't know if this issue applies for windows and if bowtie wouldn't tell you about the permission problem).

otherwise:
try to rename the files (no capital, no special chars etc) or maybe to move the read file in the same directory as your bowtie executable is:

bowtie hg18 -q myreads myreadsresults

Hm - hope something will help

[schmima]

just another idea:
if your file is large, check what happens if you split it - so that every single file is less than 2-3 GB in size.

[AVincent]

I renamed the file and tried to move it to the bowtie directory but I got the same warning again.
My files are already around 2-4GB in size so I don't really know what else I can do...
But thanks again schmima!...

[MagmaManiac]

Did you get it to work?

Hey AVicent,

Did you finally get it to work? I'm having the same problem, in Ubuntu however. Have tried moving the files to the same directory as the binary, but still getting the same "could not open read file" message. Please let me know if/how you solved this.

Thanks!

[biznatch]

When you specify file you want to process, give the entire path, like C:\directory1\directory2\file.fastq

[MagmaManiac]

Thanks biznatch, I finally got it to work. It was some small thing, I don't remember now...probably something like what you wrote.

[babaref]

Please rename the filename to hg18.fq then try the script below:

bowtie hg18 reads/hg18.fq

In windows you have to try on a computer with high memory
I recommend to try with linux

[Lcontami]

Hey,
I just spent a whole day trying to make this code work... For me the problem was that my FASTQ file's extension was fastq.
When changed for .fq, and specified in the command line,
bowtie hg18 reads/Pool7_BC1_read1.fq Pool7_BC1_read1_output.txt
it worked.

[zgtmann]

Hello everybody,

I have the same problem but I cannot solve it :-( Do you have any advice?

I couldnt even run the example bowtie (getting stared http://bowtie-bio.sourceforge.net/tutorial.shtml)...

I have in the same directory e_coli_1000.fa + indexes , e_coli_1000.fq..

When I try bowtie e_coli reads/e_coli_1000.fq it says:

Warning: Could not open read file "reads/e_coli_1000.fq" for reading; skipping...
Command: bowtie e_coli reads/e_coli_1000.fq

Thank you very much for any advice...