File "/usr/lib64/python2.4/logging/__init__.py", line 718,

[twotwo]

Hi, all,
When I want to run the tophat with bowtie2, I always got the following error message. How can I do for the tophat? Thanks!
[2012-05-15 11:38:58] Mapping left_kept_reads against hg19 with Bowtie2
Traceback (most recent call last):
File "/usr/lib64/python2.4/logging/__init__.py", line 740, in emit
self.flush()
File "/usr/lib64/python2.4/logging/__init__.py", line 718, in flush
self.stream.flush()
IOError: [Errno 5] Input/output error
[2012-05-15 12:49:43] Mapping left_kept_reads_seg1 against hg19 with Bowtie2 (1/4)
Traceback (most recent call last):
File "/usr/lib64/python2.4/logging/__init__.py", line 740, in emit
self.flush()
File "/usr/lib64/python2.4/logging/__init__.py", line 718, in flush
self.stream.flush()
IOError: [Errno 5] Input/output error

[sepulveda]

I had just ran into this problem, any suggestions?

[twotwo]

Hi,
First you need to make sure that the samtools have two folders: /lib and /include
Second, you need to run the configure command like the following. You need have LIBS option. Please let me know if it works...
./configure LIBS=-lrt --prefix=/tophat209 --with-boost=/boost_154 --with-bam=/samtools-0.1.19/samtools0119
make
make install

[sepulveda]

Hi, I found out what's wrong with mine. I accidentally have two programs running and have them output to the same folder. It caused the conflict.