Dear all,
I installed bowtie 0.12.5, tophat 1.0.13 and I have Pyhton 2.4 on my Linux.
When I launch tophat with the test files downloaded from their websites, I get this error message
$ ./tophat -r 20 ../test_data/test_ref ../test_data/reads_1.fq ../test_data/reads_2.fq
[Tue May 25 14:38:26 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Tue May 25 14:38:26 2010] Preparing output location ./tophat_out/
[Tue May 25 14:38:26 2010] Checking for Bowtie index files
[Tue May 25 14:38:26 2010] Checking for reference FASTA file
[Tue May 25 14:38:26 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Tue May 25 14:38:26 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred33 (default)
[Tue May 25 14:38:26 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:26 2010] Joining segment hits
Splitting reads into 3 segments
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Joining segment hits
Splitting reads into 3 segments
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Searching for junctions via segment mapping
[Tue May 25 14:38:27 2010] Retrieving sequences for splices
[Tue May 25 14:38:27 2010] Indexing splices
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Joining segment hits
Traceback (most recent call last):
File "./tophat", line 1635, in ?
sys.exit(main())
File "./tophat", line 1595, in main
user_supplied_juncs)
File "./tophat", line 1502, in spliced_alignment
stdout=open(merged_map,"w"))
File "/usr/lib64/python2.4/subprocess.py", line 412, in call
return Popen(*args, **kwargs).wait()
File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Any idea of what's wrong?
Thanks!
I installed bowtie 0.12.5, tophat 1.0.13 and I have Pyhton 2.4 on my Linux.
When I launch tophat with the test files downloaded from their websites, I get this error message
$ ./tophat -r 20 ../test_data/test_ref ../test_data/reads_1.fq ../test_data/reads_2.fq
[Tue May 25 14:38:26 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Tue May 25 14:38:26 2010] Preparing output location ./tophat_out/
[Tue May 25 14:38:26 2010] Checking for Bowtie index files
[Tue May 25 14:38:26 2010] Checking for reference FASTA file
[Tue May 25 14:38:26 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Tue May 25 14:38:26 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred33 (default)
[Tue May 25 14:38:26 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:26 2010] Joining segment hits
Splitting reads into 3 segments
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Joining segment hits
Splitting reads into 3 segments
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
[Tue May 25 14:38:27 2010] Searching for junctions via segment mapping
[Tue May 25 14:38:27 2010] Retrieving sequences for splices
[Tue May 25 14:38:27 2010] Indexing splices
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue May 25 14:38:27 2010] Joining segment hits
Traceback (most recent call last):
File "./tophat", line 1635, in ?
sys.exit(main())
File "./tophat", line 1595, in main
user_supplied_juncs)
File "./tophat", line 1502, in spliced_alignment
stdout=open(merged_map,"w"))
File "/usr/lib64/python2.4/subprocess.py", line 412, in call
return Popen(*args, **kwargs).wait()
File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Any idea of what's wrong?
Thanks!
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