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Old 07-22-2010, 12:11 PM   #1
AVincent
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Default Bowtie "could not open read file"

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
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Old 07-23-2010, 11:27 AM   #2
Bardj
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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.
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Old 07-23-2010, 06:53 PM   #3
sp_wade
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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!
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Old 07-30-2010, 06:34 AM   #4
AVincent
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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
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Old 07-30-2010, 07:01 AM   #5
schmima
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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
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Old 07-30-2010, 07:08 AM   #6
AVincent
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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!
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Old 07-30-2010, 07:25 AM   #7
schmima
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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
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Old 07-30-2010, 07:38 AM   #8
schmima
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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.
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Old 07-30-2010, 08:49 AM   #9
AVincent
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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!...
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Old 12-29-2010, 05:59 PM   #10
MagmaManiac
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Default 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!
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Old 01-04-2011, 01:06 PM   #11
biznatch
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When you specify file you want to process, give the entire path, like C:\directory1\directory2\file.fastq

Last edited by biznatch; 01-04-2011 at 01:11 PM.
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Old 01-04-2011, 03:12 PM   #12
MagmaManiac
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Thanks biznatch, I finally got it to work. It was some small thing, I don't remember now...probably something like what you wrote.
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Old 08-01-2011, 03:10 AM   #13
babaref
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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
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Old 02-22-2013, 04:10 PM   #14
Lcontami
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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.
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Old 04-05-2013, 03:46 AM   #15
zgtmann
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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...
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Old 04-08-2013, 04:06 AM   #16
zgtmann
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I already solved it...:-) I have had mistake in my pathway :-)
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Old 05-12-2016, 09:00 PM   #17
reprogrammer
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Yes, I had the same problem and it was solved by changing the relative path to the absolute path.

Btw, I do not know how to use Terminal and Linux, I am using Rbowtie package with R studio.
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