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Old 06-02-2010, 01:33 AM   #1
Brajbio
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Location: India

Join Date: Jun 2010
Posts: 20
Default Tophat...Mapping reads against Reference with Bowtie [FAILED]

Hi,

I am trying to run tophat with the sample data reads_1.fq and reads_2.fq.

I built the bowtie index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command

tophat -r 20 test_ref reads_1.fq reads_2.fq

and the output i got is an error showing on console

[Wed Jun 2 13:46:29 2010] Beginning TopHat run (v1.0.7)
-----------------------------------------------
[Wed Jun 2 13:46:29 2010] Preparing output location ./tophat_out/
[Wed Jun 2 13:46:29 2010] Checking for Bowtie index files
[Wed Jun 2 13:46:29 2010] Checking for reference FASTA file
[Wed Jun 2 13:46:29 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Wed Jun 2 13:46:29 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred
Splitting reads into 3 segments
[Wed Jun 2 13:46:29 2010] Mapping reads against test_ref with Bowtie
Error: could not execute Bowtie
Traceback (most recent call last):
File "/usr/bin/tophat", line 1476, in ?
sys.exit(main())
File "/usr/bin/tophat", line 1450, in main
user_supplied_juncs)
File "/usr/bin/tophat", line 1297, in spliced_alignment
unmapped_seg)
File "/usr/bin/tophat", line 612, in bowtie
exit(1)
TypeError: 'str' object is not callable
[FAILED]


Could you please help me to sort out this issue.

Thanks,
Brajendra
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