Question: Stringtie error message
0
gravatar for saj98
2.4 years ago by
saj98110
saj98110 wrote:

Hello everyone

I am using the following command which already explained in the nature protocol paper

stringtie –e –B -p 8 -G stringtie_merged.gtf -o ballgown/WS021/WS021.gtf Bam/WS021.bam

The issue it gave me the following error

Error: input file –e cannot be found!

However, when I delete -e and -B options, it run fine. Can anyone explain for me the problem? I appreciate your time and help

software error • 1.2k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.4 years ago by saj98110
1
stringtie –e –B -p 8 -G stringtie_merged.gtf -o ballgown/WS021/WS021.gtf Bam/WS021.bam

Has the above command line been copy / pasted from your scripts? Note that –e and –B (with dash) are different from -e and -B (with hyphen), and command line parameters are indicated by hyphens, not dashes.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by h.mon29k

This looks like a positional parameters/named parameters error. Maybe the program is not equipped to handle -e in the position you're passing it in?

ADD REPLYlink written 2.4 years ago by RamRS25k

Try putting the -e and -B at the end of the command, maybe.

ADD REPLYlink written 2.4 years ago by WouterDeCoster43k
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