Hi, i have some problems i don't seem to be able to solve. When i run tophat on my own machine, i dont have any problems, but when i run both a binary or a version compiled on the server on our cluster, i get the following error.
I have tried several versions of Tophat without luck.
So the big qustions: Do anyone know which directory it lacks?
The run.log is not of much help
[2013-08-06 11:52:08] Building transcriptome data files..
[2013-08-06 11:52:21] Building Bowtie index from btindex.fa
[2013-08-06 12:01:30] Mapping left_kept_reads to transcriptome btindex with Bowtie2
[2013-08-06 12:05:17] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "/package/bio/tophat/src/tophat", line 4072, in ?
sys.exit(main())
File "/package/bio/tophat/src/tophat", line 4038, in main
user_supplied_deletions)
File "/package/bio/tophat/src/tophat", line 3446, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "/package/bio/tophat/src/tophat", line 1155, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.4/subprocess.py", line 550, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 996, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
~
I i am running TopHat (v2.0.9), Bowtie 2.1.0.0 and Samtools 0.1.18.0
I have tried several versions of Tophat without luck.
So the big qustions: Do anyone know which directory it lacks?
The run.log is not of much help
[2013-08-06 11:52:08] Building transcriptome data files..
[2013-08-06 11:52:21] Building Bowtie index from btindex.fa
[2013-08-06 12:01:30] Mapping left_kept_reads to transcriptome btindex with Bowtie2
[2013-08-06 12:05:17] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "/package/bio/tophat/src/tophat", line 4072, in ?
sys.exit(main())
File "/package/bio/tophat/src/tophat", line 4038, in main
user_supplied_deletions)
File "/package/bio/tophat/src/tophat", line 3446, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "/package/bio/tophat/src/tophat", line 1155, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.4/subprocess.py", line 550, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 996, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
~
I i am running TopHat (v2.0.9), Bowtie 2.1.0.0 and Samtools 0.1.18.0
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