Tophat :OSError: [Errno 2] No such file or directory: '/tmp/segment.juncs

[jiangs]

Greetings,
I'm new to tophat, here is my problem and I really need your help.
My command is tophat2 -o NA06993 -G Ensemble.655.gtf -a 8 -m 0 -I 300000 -p 2 -g 20 --library-type fr-unstranded --fusion-read-mismatches 3 /rd/data/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome SRR032239.fastq

The error information is :
Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
Traceback (most recent call last):
File "/rd/tools_centos6.3/build/tophat-2.0.9/install/bin/tophat", line 4072, in <module>
sys.exit(main())
File "/rd/tools_centos6.3/build/tophat-2.0.9/install/bin/tophat", line 4038, in main
user_supplied_deletions)
File "/rd/tools_centos6.3/build/tophat-2.0.9/install/bin/tophat", line 3614, in spliced_alignment
if os.path.getsize(juncs[0]) != 0:
File "/usr/lib64/python2.6/genericpath.py", line 49, in getsize
return os.stat(filename).st_size
OSError: [Errno 2] No such file or directory: 'NA06993/tmp/segment.juncs'

So how can I fix this?

[genome1]

I am also facing similar problem while running tophat2.
I am using tophat2 (v2.0.11) and Bowtie2 (v2.2.2).
I am using default parameters while running tophat. My command line is:
$ tophat -G /path/to/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf -o /path/to/out -p 8 /path/to/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome /path/to/read_1.fastq.gz /path/to/read_2.fastq.gz

The last few lines of the error message is:

[2014-04-18 01:59:45] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4084, in <module>
sys.exit(main())
File "./tophat", line 4050, in main
user_supplied_deletions)
File "./tophat", line 3452, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1159, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Can anyone help me to solve the problem.
Thank you.

[GenoMax]

Is this a new install? If it is, have you tested it with the sample data to ensure everything is working properly.

[genome1]

The problem has been resolved.
Now I have used tophat2 instead of tophat in my command line.