an error when using tophat

[masylichu]

[wgf@world SRA_shortreads]$ tophat.py ../ws190_index/C.elegans.ws190.dna SRR019978.fastq

[Fri Oct 29 15:26:03 2010] Beginning TopHat run (v1.1.1)
-----------------------------------------------
[Fri Oct 29 15:26:03 2010] Preparing output location ./tophat_out/
[Fri Oct 29 15:26:03 2010] Checking for Bowtie index files
[Fri Oct 29 15:26:03 2010] Checking for reference FASTA file
[Fri Oct 29 15:26:03 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Oct 29 15:26:03 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Fri Oct 29 15:26:05 2010] Checking reads
min read length: 37bp, max read length: 37bp
format: fastq
quality scale: phred33 (default)
Error locating program: prep_reads


what is the problem?

[repinementer]

how did you setup bowtie and tophat

[masylichu]

how did you setup bowtie and tophat

i download the bowtie and use this program to map the short reads successfully.

i also download the tophat (v1.1.1) and make install according to the manual.

In the /src directory, there is tophat.py to run.First time, i have run the tophat successfully, and the result is in the /tophat_out directory.

after that, i change a larger fastq file, the error occurs.

[wgf@world src]$ tophat.py ~/bowtie/ws190_index/C.elegans.ws190.dna ~/bowtie/SRA_shortreads/SRR019978.fastq

[Fri Oct 29 18:16:05 2010] Beginning TopHat run (v1.1.1)
-----------------------------------------------
[Fri Oct 29 18:16:05 2010] Preparing output location ./tophat_out/
[Fri Oct 29 18:16:05 2010] Checking for Bowtie index files
[Fri Oct 29 18:16:05 2010] Checking for reference FASTA file
[Fri Oct 29 18:16:05 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Oct 29 18:16:05 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Fri Oct 29 18:16:07 2010] Checking reads
min read length: 37bp, max read length: 37bp
format: fastq
quality scale: phred33 (default)
Error locating program: prep_reads

[Daehwan]

Did you run "make install"? If yes, you can run tophat using your_tophat_directory/bin/tophat.

Otherwise, there should be some problem regarding TopHat installation.

[masylichu]

Did you run "make install"? If yes, you can run tophat using your_tophat_directory/bin/tophat.

Otherwise, there should be some problem regarding TopHat installation.

thank you. i have solved this problem.

[lfaino]

error

Hi masylichu,
how did you solve the problem? I have the same error.

Luigi

[masylichu]

hello, Luigi

That may be the problem of samtools installation.

please you check your installation of samtools, meanwhile, follow the instruction of tophat software.