Tophat can and can't find bowtie???

[chris.cornelison]

Judging from the output, Tophat is able to determine the version of bowtie and call bowtie-inspect to reconstitute the fasta from the index, but can't seem to locate bowtie???? All bowtie executables are in the path as are the samtools.

[Mon Nov 1 14:27:34 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Mon Nov 1 14:27:34 2010] Preparing output location ./tophat_out/
[Mon Nov 1 14:27:34 2010] Checking for Bowtie index files
[Mon Nov 1 14:27:34 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /sbs/genomes/bowtie/ZmChrBuild_PHIv2.fa
[Mon Nov 1 14:27:34 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Nov 1 14:42:48 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Mon Nov 1 14:42:48 2010] Checking for Samtools
[FAILED]
Error: bowtie not found on this system


Any ideas?

Thanks,
Chris

[kopi-o]

I would guess it's not finding samtools and that the error message is imprecise.

[chris.cornelison]

That was my thought as well. Just a red herring. Anyone have any thoughts on the vague [FAILED] message regarding samtools. I was able to build the samtools and tophat successfully.

Thanks,
Chris

[KevinLam]

I would guess it's not finding samtools and that the error message is imprecise.

Yups I can confirm this.
had the same problem too.
was easier for me to find out as i ran this as a remote job using PBS, it occured to me instantly that I didn't put the binaries there so i checked both turns out it was samtools that was missing not bowtie.

[chris.cornelison]

So I guess the real question is, where is Tophat expecting to find the samtools? They are in the path. The installation of these tools and their dependencies really needs to be cleaned up.

Chris

[Daehwan]

So I guess the real question is, where is Tophat expecting to find the samtools? They are in the path. The installation of these tools and their dependencies really needs to be cleaned up.

Chris

TopHat expects samtools just like bowtie. (sorry for the incorrect error message)

And TopHat runs samtools, which gives the following message on my server:

============================================
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.7 (r510)

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
pileup generate pileup output
faidx index/extract FASTA
tview text alignment viewer
index index alignment
fixmate fix mate information
glfview print GLFv3 file
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates
============================================

As you see in the above, TopHat checks the version of samtools from the string "Version: 0.1.7 (r510)". So, I think there are two possibilities: either (1) samtools is not in "path" or (2) "version" string doesn't exist.

[chris.cornelison]

Hmmm. If I run samtools.pl the version output looks quite a bit different from yours. Is tophat compatible with the latest version of samtools 0.1.9?

[compbio@lx42 samtools-0.1.9]$ samtools.pl

Program: samtools.pl (helper script for SAMtools)
Version: 0.3.3
Contact: Heng Li <[email protected]>

Usage: samtools.pl <command> [<arguments>]

Command: varFilter filtering SNPs and short indels
pileup2fq generate fastq from `pileup -c'
showALEN print alignment length (ALEN) following CIGAR

Thanks,
Chris

[Daehwan]

Hmmm. If I run samtools.pl the version output looks quite a bit different from yours. Is tophat compatible with the latest version of samtools 0.1.9?

[compbio@lx42 samtools-0.1.9]$ samtools.pl

Program: samtools.pl (helper script for SAMtools)
Version: 0.3.3
Contact: Heng Li <[email protected]>

Usage: samtools.pl <command> [<arguments>]

Command: varFilter filtering SNPs and short indels
pileup2fq generate fastq from `pileup -c'
showALEN print alignment length (ALEN) following CIGAR

Thanks,
Chris

TopHat runs "samtools" instead of "samtools.pl" - it's probably because you didn't install samtools like "make install" (although I never installed samtools myself before).

[chris.cornelison]

The problem was that I followed the samtools installation instruction exactly.


Installation
============

Simply copy `samtools' and other executables/scripts in `misc' to a
location you want (e.g. a directory in your $PATH). No further
configurations are required.

Make doesn't build the 'samtools' executable into the 'misc' directory.

Chris

[Daehwan]

The problem was that I followed the samtools installation instruction exactly.


Installation
============

Simply copy `samtools' and other executables/scripts in `misc' to a
location you want (e.g. a directory in your $PATH). No further
configurations are required.

Make doesn't build the 'samtools' executable into the 'misc' directory.

Chris

I see, samtools is actually different from samtools.pl - samtools is located under your_samtools_directory instead of your_samtools_directory/misc