Proper installation of TopHat with Bowtie

[zorph]

so I work in an institution where the CCS dept is responsible for installation.

When trying to run TopHat, I get this output:

[Wed May 26 20:18:38 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed May 26 20:18:38 2010] Preparing output location ./tophat_out/
[Wed May 26 20:18:38 2010] Checking for Bowtie index files
[Wed May 26 20:18:38 2010] Checking for reference FASTA file
[Wed May 26 20:18:38 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system


the way they installed tophat and bowtie is the following:
../a/b.directory_c/tophat/1.0.13/bin/tophat (stuff)
../a/b/directory_c/bowtie/0.12.5/bowtie (stuff)

while I wouldn't mind moving stuff around to figure out how to get things to work, having them do it is painful (and time consuming). Can someone tell me how they ought to be orientated to run top hat properly

[john_mu]

Hi zorph,

You need to put bowtie in your path directory or the same directory as tophat.

eg. if TopHat is in ~/programs/

You also need to put Bowtie in ~/programs/

---

Alternatively, you can put both in your "bin" folder such as

/usr/bin

If you do this, then you can run TopHat or Bowtie without specifying the path to the executable.

EDIT: when I say put, I mean only move the executables there, not anything else and don't create any additional folders.

[raela]

You could also alter your PATH to include the bowtie directory. It depends on the shell you use (in linux, use `env | grep SHELL` to determine which this is). For example, bash is the default shell on my system, so in ~/.bashrc I have "export PATH=$PATH:/usr/local/genome/bin". You could add a similar line and point it to bowtie's location.

[zorph]

You could also alter your PATH to include the bowtie directory. It depends on the shell you use (in linux, use `env | grep SHELL` to determine which this is). For example, bash is the default shell on my system, so in ~/.bashrc I have "export PATH=$PATH:/usr/local/genome/bin". You could add a similar line and point it to bowtie's location.

Thank you so much for this piece of advice. Using it, I was able to get the test-reads to run; however, I was unable to get MY reads to run (see error message below).

I gather there is something wrong with my reads. The sample is from solid and i used a script to convert them to a fastq format. The head of my fastq file is below the error message.

Any help would be much appreciated. Thank YOU!

ERROR MESSAGE

[Thu Jun 3 12:57:27 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Thu Jun 3 12:57:27 2010] Preparing output location ./tophat_out/
[Thu Jun 3 12:57:27 2010] Checking for Bowtie index files
[Thu Jun 3 12:57:27 2010] Checking for reference FASTA file
[Thu Jun 3 12:57:27 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Thu Jun 3 12:57:27 2010] Checking reads
seed length: 49bp
format: fastq
quality scale: phred33 (default)
[FAILED]
Error: could not execute prep_reads
Traceback (most recent call last):
File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 1635, in ?
sys.exit(main())
File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 1575, in main
"left_kept_reads")
File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 799, in prep_reads
exit(1)
TypeError: 'str' object is not callable

FASTQ FILE

cat out.martin_ct8_d3.single.fq | head
@/mihg/users/chumphries2/out.martin_ct8_d3:1_11_30/1
CTNCGNNGNGNNNTGNNNAGNNNATCNTNGNGNCNNGNNGNGTCGNANC
+
-"%1-"(%-"-")-"%-"-"-"1%-"-"-"/%-"-"-"+%*-")-"&-")-"&-"-",-"-"%-"&'%%-")-"&
@/mihg/users/chumphries2/out.martin_ct8_d3:1_12_50/1
TGGGCNGGTGNGGGGNNNCCNNTCCCCGGGNCNGGNGGGGNGCGCNCNC
+

[raela]

I would try another script to convert your files. I haven't done anything with solid myself, so I don't have any advice there, but the reads you posted didn't convert very well. There should be a logs/ directory in the tophat output directory with more information as to why it failed, but I'm suspicious of all of the Ns/low quality calls.

[Timothy Amos]

This error can mean "correct version of bowtie not found"

[Wed May 26 20:18:38 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system

I recently got the same error:

[2014-09-17 11:33:06] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

However, my issue was that the HPC admin had updated (the default version of) bowtie to a version that wasn't compatible with the installed version of tophat.
I fixed this my removing that module and loading the old one (i.e. changing which version of bowtie was referred to on my path).

http://ccb.jhu.edu/software/tophat/index.shtml lists which version of bowtie is compatible with which version of tophat.