Entering edit mode
11.1 years ago
zhangpeng1334880
•
0
The command I am using is as follows:
tophat -G /Users/zhang/Desktop/humantophat\ /genes.gtf -o B5thout /Users/zhang/Desktop/humantophat\ /genome /Users/zhang/Desktop/humantophat\ /BrM5.fastq.
The result is
[2013-10-12 02:26:06] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-10-12 02:26:06] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-10-12 02:26:06] Checking for Samtools
Samtools version: 0.1.18.0
[2013-10-12 02:26:06] Checking for Bowtie index files (genome)..
[2013-10-12 02:26:06] Checking for reference FASTA file
[2013-10-12 02:26:06] Generating SAM header for /homea4/zhangls/zp/tophat/genome
format: fastq
quality scale: phred33 (default)
[2013-10-12 02:26:07] Reading known junctions from GTF file
[FAILED]
[Errno 8] Exec format error
When I run the command on my PC, everything works fine. But it fails on the server. All the data are the same. Why is this happening?
This sounds like a difference in text formats. Mostly likely your PC and server are using different ASCII encoding for line-breaks. Try doing this with your file:
Dear Damian Kao ,I tried tr -d '\r' < file.gtf > formatted.gtf,but it does not work. The problem still exit.
When you open the genes.gtf file in
vim
, do you see little blue^M
characters at the end of every line?I use the editor sublime, there is no ^M characters at the end of the line.
Can you post the output of
head genes.gtf
?if you post a Dropbox link to the file, I'll download it and have a look at it.
OK, looking at your command line again, I see that you're escaping a space at the end of your
humantophat
directory. Is there really a space at the end of that directory? Can you post the output ofls /Users/zhang/Desktop/humantophat\ /
?