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?
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?
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