Bowtie, Tophat and Python

[TGBelgard]

This may be because the 'sort' command (and probably the rest of the default system-wide bin) cannot be found in your PATH. Check that your $PATH environment variable is properly set (be careful to append or prepend additional PATH locations rather than overwrite).

[Enrico Palazzo]

same problem

Hi,

did you find a reason for this error? I get the same error running

tophat -p 8 --output-dir output/26_1 genome/Homo
_sapiens.hg19/hg19 readfiles/s_100617_3_1.fastq

******************************************************
Error log:
[Mon Oct 25 10:44:10 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Oct 25 10:44:10 2010] Preparing output location output/26_1/
[Mon Oct 25 10:44:10 2010] Checking for Bowtie index files
[Mon Oct 25 10:44:10 2010] Checking for reference FASTA file
[Mon Oct 25 10:44:10 2010] Checking for Bowtie
Bowtie version: 0.12.1.0
[Mon Oct 25 10:44:10 2010] Checking reads
seed length: 51bp
format: fastq
quality scale: phred33 (default)
[Mon Oct 25 10:54:50 2010] Mapping reads against hg19 with Bowtie
[Mon Oct 25 11:30:57 2010] Joining segment hits
Splitting reads into 2 segments
[Mon Oct 25 11:42:02 2010] Mapping reads against hg19 with Bowtie
[Mon Oct 25 11:47:40 2010] Mapping reads against hg19 with Bowtie
[Mon Oct 25 11:52:33 2010] Searching for junctions via segment mapping
[Mon Oct 25 12:01:35 2010] Retrieving sequences for splices
[Mon Oct 25 12:04:01 2010] Indexing splices
[Mon Oct 25 12:23:04 2010] Mapping reads against segment_juncs with Bowtie
[Mon Oct 25 12:26:55 2010] Mapping reads against segment_juncs with Bowtie
[Mon Oct 25 12:30:42 2010] Joining segment hits
Traceback (most recent call last):
File "tophat", line 1635, in <module>
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/python2.6/subprocess.py", line 444, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib64/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1106, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
******************************************************

Last entry in run.log was:

sort -k 1,1n --temporary-directory=output/26_1/tmp/ output/26_1/tmp/file
vsmUly output/26_1/left_kept_reads.fq.candidate_hits.sam > output/26_1/tmp/file5jC6td

file5jC6td have been created in tmp/ but it's empty.

Any suggestions?

Thanks

[natpokah]

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!