Reading Known Junctions From Gtf File Failed

Question

[zhangpeng1334880]

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?

[Damian Kao]

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:

tr -d '\r' < file.gtf > formatted.gtf

[zhangpeng1334880]

Dear Damian Kao ,I tried tr -d '\r' < file.gtf > formatted.gtf,but it does not work. The problem still exit.

[Dan D]

When you open the genes.gtf file in vim, do you see little blue ^M characters at the end of every line?

[zhangpeng1334880]

I use the editor sublime, there is no ^M characters at the end of the line.

[Dan D]

Can you post the output of head genes.gtf?

[Dan D]

if you post a Dropbox link to the file, I'll download it and have a look at it.

[Dan D]

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 of ls /Users/zhang/Desktop/humantophat\ /?

Answer 1

[zhangpeng1334880]

Thanks a lot. I think I have found the key to the problem. I use the wrong version of the tophat.