Hi everyone
I'm rather new to this field, so am trying my best and have spent the better part of a day trying to get Tophat2 to work with RNA-seq data and the hg19 reference. I can smell that I'm close, but I just don't or can't see what is wrong with the way I'm running the program. I have installed everything as per instructions, the programs are all in the path, the indexes installed, and so I start with the following:
which gives
[2012-05-09 09:20:23] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-09 09:20:23] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-05-09 09:20:23] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-09 09:20:23] Checking for Bowtie index files
[2012-05-09 09:20:23] Checking for reference FASTA file
[2012-05-09 09:20:23] Generating SAM header for /home/thompsonl/programs/bowtie2/hg19
Traceback (most recent call last):
File "/home/thompsonl/programs/tophat2/tophat", line 3778, in ?
sys.exit(main())
File "/home/thompsonl/programs/tophat2/tophat", line 3645, in main
params.read_params = check_reads_format(params, reads_list)
File "/home/thompsonl/programs/tophat2/tophat", line 1676, in check_reads_format
zf = ZReader(f_name, params.system_params)
File "/home/thompsonl/programs/tophat2/tophat", line 1629, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''
Now obviously, it can't find something, but what exactly can't it find ? I've checked the logs in the output directory but that doesn't yield any additional info. I've also tried a precompiled and source version of tophat2, but it doesn't seem to make a difference.
Any suggestions for my myopia ?
Thanks
Liam
I'm rather new to this field, so am trying my best and have spent the better part of a day trying to get Tophat2 to work with RNA-seq data and the hg19 reference. I can smell that I'm close, but I just don't or can't see what is wrong with the way I'm running the program. I have installed everything as per instructions, the programs are all in the path, the indexes installed, and so I start with the following:
Code:
tophat2 -p 4 -o hivA --library-type fr-firststrand --keep-tmp --b2-very-sensitive $HOME/programs/bowtie2/hg19 $HOME/lincrna/fastq/A_1.fastq, $HOME/lincrna/fastq/A_2.fastq
[2012-05-09 09:20:23] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-09 09:20:23] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-05-09 09:20:23] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-09 09:20:23] Checking for Bowtie index files
[2012-05-09 09:20:23] Checking for reference FASTA file
[2012-05-09 09:20:23] Generating SAM header for /home/thompsonl/programs/bowtie2/hg19
Traceback (most recent call last):
File "/home/thompsonl/programs/tophat2/tophat", line 3778, in ?
sys.exit(main())
File "/home/thompsonl/programs/tophat2/tophat", line 3645, in main
params.read_params = check_reads_format(params, reads_list)
File "/home/thompsonl/programs/tophat2/tophat", line 1676, in check_reads_format
zf = ZReader(f_name, params.system_params)
File "/home/thompsonl/programs/tophat2/tophat", line 1629, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''
Now obviously, it can't find something, but what exactly can't it find ? I've checked the logs in the output directory but that doesn't yield any additional info. I've also tried a precompiled and source version of tophat2, but it doesn't seem to make a difference.
Any suggestions for my myopia ?
Thanks
Liam
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