tophat run Failed...

[doolll]

hi everyone,
I'm a beginner of linux
I have a problem with running tophat.


[2013-02-26 18:47:24] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-26 18:47:24] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.9.0
[2013-02-26 18:47:24] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-26 18:47:24] Checking for Bowtie index files
Warning: we do not recommend to have both Bowtie1 and Bowtie2 indexes in the same directory
the genome sequence (*.fa) may not be compatible with one of them
[2013-02-26 18:47:24] Checking for reference FASTA file
[2013-02-26 18:47:24] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2013-02-26 18:47:24] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2013-02-26 18:47:24] Mapping left_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Mapping right_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.52.0: cannot open shared object file: No such file or directory


If anybody know, please give a comment...
thanks,

[iris_aurelia]

Have you added boost to your path? Maybe you should try the following:

export LD_LIBRARY_PATH=/boostdir/boost/dist/lib/

[doolll]

Thanks, iris_aurelia

you mean..
/boostdir/boost/dist/lib/
is the boost prefix directory??

I did like this:
export LD_LIBRARY_PATH=/usr/local/bin/lib/

but still error=127 is comming.

and i dont know what the "LD_LIBRARY" is.

[iris_aurelia]

Yes, you should give it the path where your boost files are stored.

[AsoBioInfo]

Can you post the TopHat commmand?

[doolll]

I just want to check install stat, so I using test file.

following is the tophat command:
tophat -r 20 test_ref reads_1.fq reads_2.fq

than i got the error message (error=127).


And my boost prefix directory(/usr/local/bin/lib/) have


libboost_chrono.a libboost_locale.a libboost_prg_exec_monitor.a libboost_system.a libboost_context.a libboost_math_c99.a libboost_program_options.a libboost_test_exec_monitor.a
libboost_date_time.a libboost_math_c99f.a libboost_python.a libboost_thread.a libboost_exception.a libboost_math_c99l.a libboost_random.a libboost_timer.a libboost_filesystem.a libboost_math_tr1.a libboost_regex.a libboost_unit_test_framework.a
libboost_graph.a libboost_math_tr1f.a libboost_serialization.a
libboost_wave.a libboost_iostreams.a libboost_math_tr1l.a libboost_signals.a libboost_wserialization.a

these kind of files, do u know this is right? I dont know whether it correct or not...

thank you guys!

[Luyi Tian]

It seems you don't have libboost_thread.so.1.52.0 in your directory.
If you are not familiar with linux I suggest you install a pre-compiled binary release, instead of build it from source. So you don't need boost lib anymore.
this is the tutorial:

http://tophat.cbcb.umd.edu/tutorial.html