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Old 11-12-2010, 11:27 AM   #1
pettervikman
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Location: Sweden

Join Date: Nov 2009
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Default Bow-tie inspect returned an error

Hi all

I'm trying to run TopHat for the first time. I've checked the installation with the complementary test data set and that worked. Now with my own data set I get that message right after it tries to create the rat rn4.fa file since it's lacking in the index_folder. I've downloaded and unpacked the files from the bowtie/tophat webpage and I ran the make script. I've asked our IT people but since they are even more unfamiliar then me (which says a lot) with this program I got no help.

So any help would be greatly appreciated! I 've pasted the entire message from TopHat below.

Sincerely

/Petter

[1] 19633
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:30 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:30 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:30 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr*.*
tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_* &
[2] 19634
[1] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr* s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:40 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:40 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:40 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr.*
tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_* &
[3] 19635
[2] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:47 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:47 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:47 2010] Checking for Bowtie index files
[Fri Nov 12 19:28:47 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /data/archive/bowtie-indexes/rn4.fa
[Fri Nov 12 19:28:47 2010] Reconstituting reference FASTA file from Bowtie index
[FAILED]
Error: bowtie-inspect returned an error

[3]+ Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_*
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Old 11-14-2010, 02:25 AM   #2
reut
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Default I have the same problem

Hi
I am new to this too.
also trying to run Tophat v1.1.2 with Bowtie v0.12.7.0 and get the same error message -
Code:
[Sun Nov 14 12:15:36 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Sun Nov 14 12:15:36 2010] Preparing output location ./tophat_out/
[Sun Nov 14 12:15:36 2010] Checking for Bowtie index files
[Sun Nov 14 12:15:36 2010] Checking for reference FASTA file
        Warning: Could not find FASTA file /bowtie-0.12.7/indexes/mm9.fa
[Sun Nov 14 12:15:36 2010] Reconstituting reference FASTA file from Bowtie index
Executing: bowtie-inspect mm9 > ./tophat_out/mm9.fa
        [FAILED]
Error: bowtie-inspect returned an error
when I run an older version - Tophat v1.0.12 and Bowtie v0.10.0.0 it does succeed.

Last edited by reut; 11-14-2010 at 10:49 PM.
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Old 11-15-2010, 06:07 AM   #3
pettervikman
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Default

Thanks for the tip. I've asked our IT department to install the older versions. Is there somewhere I can get them from? Question two, are we the only ones with this issue? Because if others are able to get the whole thing to work maybe installing the older software is a less then optimal workaround.

Is there someone that's been able to get bowtie/tophat to work versus the rat genome using the latest installations of the software together with the latest genomes from the bowtie manual page?
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Old 11-16-2010, 12:08 AM   #4
reut
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Default older Tophat versions

You can download older versions from here:
http://tophat.cbcb.umd.edu/downloads/

What I finally did was run the bowtie-inspect manually to create the .fa file (bowtie-inspect index_prefix),
copied the .fa file to the BOWTIE_INDEXES directory and then run Tophat.

Anyone else encountered this issue?
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Old 11-16-2010, 04:01 AM   #5
pettervikman
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Default

Thanks for the tip. I ran bowtie-inspect manually as well and managed to create the .fa file. I then proceeded to convert my qseqs to fastq using a perl script from (http://seqanswers.com/forums/showthread.php?t=1655). What suprised me was that the converter only created two (large) files, one per pair and lane from my paired end run. Anyway, I've now started tophat and I've gotten further then before, it's now on mapping reads.
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Old 11-17-2010, 10:48 AM   #6
tleonardi
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Default

It looks like the problem has to do with the path to the indexes files. Running

tophat /full/path/to/indexes/m_musculus reads1.fq,reads2.fq,reads3.fq

or if you have a variable to the indexes path:

tophat $BOWTIE_INDEXES/m_musculus reads1.fq,reads2.fq,reads3.fq

did the trick for me


Hope this can be helpful!

Last edited by tleonardi; 11-18-2010 at 12:46 PM.
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Old 06-27-2011, 09:07 AM   #7
camelbbs
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Default

hi,

i have the same problem. and if i use the full path, then it will be ok. but there is still an error like:


Warning: junction database is empty!

at last the bam file is very small.

anyone can help me?

Last edited by camelbbs; 06-27-2011 at 09:30 AM.
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Old 06-27-2011, 09:19 AM   #8
camelbbs
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Default

Quote:
Originally Posted by reut View Post
You can download older versions from here:
http://tophat.cbcb.umd.edu/downloads/

What I finally did was run the bowtie-inspect manually to create the .fa file (bowtie-inspect index_prefix),
copied the .fa file to the BOWTIE_INDEXES directory and then run Tophat.

Anyone else encountered this issue?
can i ask how to create the .fa file?
is bowtie-inspect mm9.1.ebwt mm9.2.ebwt mm9.3.ebwt mm9.4.ebwt?
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Old 07-13-2011, 01:41 AM   #9
louis7781x
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Default how to place samtools in "PATH" for use with TopHat on MAC

Hi everyone

Now I have installed tophat on mac64bit,but I have some question.

I download tophat-1.31 Mac OS X x86_64 binary,and it doesn't need to compile.

Quote:
You will also need the samtools program in your PATH, and if you plan to compile Tophat from source you should also install the SAM tools package, by following these steps:
Download the SAM tools
Unpack the SAM tools tarball and cd to the SAM tools source directory.
Build the SAM tools by typing make at the command line.
Choose a directory into which you wish to copy the SAM tools binary, the included library libbam.a, and the library headers. A common choice is /usr/local/.
Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
Copy the samtools binary to some directory in your PATH.
To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.2.0.tar.gz
cd tophat-1.2.0/
Now build the package:
./configure --prefix=/path/to/install/directory/
Note: If you copied the SAM tools library and header files to someplace other than /usr/local/, you may need to supply the --with-bam configuration option. For example, if you placed the libbam.a files in /opt/biotools/lib/ and SAM tools .h files in /opt/biotools/include/bam/ then the configure command will become something like this:
./configure --prefix=/opt/biotools --with-bam=/opt/biotools
(in this example tophat and its modules will be installed in /opt/biotools/bin/ directory)
After the configure script finishes successfully, build the Tophat package:
make
Finally, install TopHat:
make install
This will install tophat and its modules into /path/to/install/directory/bin directory. You may want to add that directory to your shell's PATH if it's not there already.
My question is tophat 64 bit doesn't need to compile.

How do I ./configure --prefix=..../../.

And when I run tophat,it shows the error
Quote:

[Wed Jul 13 16:28:25 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Wed Jul 13 16:28:25 2011] Preparing output location ./tophat_out/
[Wed Jul 13 16:28:25 2011] Checking for Bowtie index files
[Wed Jul 13 16:28:25 2011] Checking for reference FASTA file
[Wed Jul 13 16:28:25 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jul 13 16:28:25 2011] Checking for Samtools
Error locating program: samtools
If anyone know how to solve

Please tell me.

Thanks
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