tophat error

[pinki999]

Hi,

I am using tophat to map the RNA-seq data. But, I am getting the following error:

[Mon Jan 16 13:57:58 2012] Mapping left_kept_reads against hg19male with Bowtie

gzip: stdout: Broken pipe
[Mon Jan 16 13:57:58 2012] Processing bowtie hits
Traceback (most recent call last):
File "/work_F0/software/external/tophat-1.4.0.Linux_x86_64/tophat", line 3052, in <module>
sys.exit(main())
File "/work_F0/software/external/tophat-1.4.0.Linux_x86_64/tophat", line 3018, in main
user_supplied_deletions)
File "/work_F0/software/external/tophat-1.4.0.Linux_x86_64/tophat", line 2591, in spliced_alignment
segment_len)
File "/work_F0/software/external/tophat-1.4.0.Linux_x86_64/tophat", line 1974, in split_reads
zreads = ZReader(reads_filename, params.system_params, False)
File "/work_F0/software/external/tophat-1.4.0.Linux_x86_64/tophat", line 1268, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: './tophat_out/tmp/left_kept_reads_unmapped.fq'

Can anyone help me to get through this?

Thanks in advance.

[sphil]

As stated in the error log 'IOError: [Errno 2] No such file or directory: './tophat_out/tmp/left_kept_reads_unmapped.fq'' i would mention that the file 'left_lept_reads_unmapped.fq' isn't at it's desired place.
Can you check it?

[pinki999]

Solved the problem. There was a problem with the reference file.

Thanks