TOPHAT ,Error locating program: prep_reads

[chenyao]

Dear all,

I have a problem of using TOPHAT:


[Fri Jul 22 17:37:28 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Fri Jul 22 17:37:28 2011] Preparing output location ./tophat_out/
[Fri Jul 22 17:37:28 2011] Checking for Bowtie index files
[Fri Jul 22 17:37:28 2011] Checking for reference FASTA file
[Fri Jul 22 17:37:28 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Jul 22 17:37:28 2011] Checking for Samtools
Samtools Version: 0.1.17
[Fri Jul 22 17:37:28 2011] Generating SAM header for test_ref
[Fri Jul 22 17:37:28 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
Error locating program: prep_reads

[disciple]

I also have the same error! Can anyone help?

[Wed Aug 17 19:41:10 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Wed Aug 17 19:41:10 2011] Preparing output location /d/RNAseq/Tophat/
[Wed Aug 17 19:41:10 2011] Checking for Bowtie index files
[Wed Aug 17 19:41:10 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /d/database/hg19/hg19_c.fa
[Wed Aug 17 19:41:10 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /d/bowtie-0.12.7/bowtie-inspect /d/database/hg19/hg19_c > /d/RNAseq/Tophat/tmp/hg19_c.fa
[Wed Aug 17 19:45:47 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Aug 17 19:45:47 2011] Checking for Samtools
Samtools Version: 0.1.17
[Wed Aug 17 19:45:47 2011] Generating SAM header for /d/database/hg19/hg19_c
[Wed Aug 17 19:45:51 2011] Preparing reads
format: fasta
Error locating program: prep_reads

[chenyao]

I also have the same error! Can anyone help?

[Wed Aug 17 19:41:10 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Wed Aug 17 19:41:10 2011] Preparing output location /d/RNAseq/Tophat/
[Wed Aug 17 19:41:10 2011] Checking for Bowtie index files
[Wed Aug 17 19:41:10 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /d/database/hg19/hg19_c.fa
[Wed Aug 17 19:41:10 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /d/bowtie-0.12.7/bowtie-inspect /d/database/hg19/hg19_c > /d/RNAseq/Tophat/tmp/hg19_c.fa
[Wed Aug 17 19:45:47 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Aug 17 19:45:47 2011] Checking for Samtools
Samtools Version: 0.1.17
[Wed Aug 17 19:45:47 2011] Generating SAM header for /d/database/hg19/hg19_c
[Wed Aug 17 19:45:51 2011] Preparing reads
format: fasta
Error locating program: prep_reads

I fix this error by Add samtools “/path/to/install/directory/bin” into shell PATH.

or you can export your tophat path into PATH

Check this post http://seqanswers.com/forums/showthread.php?t=12688