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Old 04-09-2010, 09:40 AM   #1
clariet
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Location: NJ

Join Date: Mar 2010
Posts: 18
Default a tophat running problem

I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
[Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
[Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
[Fri Apr 9 13:17:33 2010] Checking for Bowtie
Bowtie version: 0.12.4.0
[Fri Apr 9 13:17:33 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred33 (default)
[Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Joining segment hits
Splitting reads into 3 segments
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Joining segment hits
Splitting reads into 3 segments
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
[Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
[Fri Apr 9 13:17:34 2010] Indexing splices
Traceback (most recent call last):
File "../bin/tophat", line 1635, in ?
sys.exit(main())
File "../bin/tophat", line 1595, in main
user_supplied_juncs)
File "../bin/tophat", line 1456, in spliced_alignment
ref_fasta)
File "../bin/tophat", line 981, in build_juncs_index
external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
File "../bin/tophat", line 943, in build_juncs_bwt_index
exit(1)
TypeError: 'str' object is not callable
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Old 04-12-2010, 05:05 AM   #2
clariet
Member
 
Location: NJ

Join Date: Mar 2010
Posts: 18
Default

Please help me out. I am sure many people here has experience with tophat. Could you please point me to the right direction how I could fix it?


Quote:
Originally Posted by clariet View Post
I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
[Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
[Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
[Fri Apr 9 13:17:33 2010] Checking for Bowtie
Bowtie version: 0.12.4.0
[Fri Apr 9 13:17:33 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred33 (default)
[Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Joining segment hits
Splitting reads into 3 segments
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Joining segment hits
Splitting reads into 3 segments
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
[Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
[Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
[Fri Apr 9 13:17:34 2010] Indexing splices
Traceback (most recent call last):
File "../bin/tophat", line 1635, in ?
sys.exit(main())
File "../bin/tophat", line 1595, in main
user_supplied_juncs)
File "../bin/tophat", line 1456, in spliced_alignment
ref_fasta)
File "../bin/tophat", line 981, in build_juncs_index
external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
File "../bin/tophat", line 943, in build_juncs_bwt_index
exit(1)
TypeError: 'str' object is not callable
clariet is offline   Reply With Quote
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