Question: Why does this happen (see image)
0
gravatar for mschmid
2.4 years ago by
mschmid0
Switzerland
mschmid0 wrote:

Sorry, I guess the solution is simple, but did not find out:

It seems that galaxy can not access the output of the applications, but why?

Here some of the errors I get:

For MUMerplot:

rm: cannot remove `out.fplot': No such file or directory
rm: cannot remove `out.rplot': No such file or directory

For nucmer DNA MUMerplot:

rm: cannot remove `out.fplot': No such file or directory
rm: cannot remove `out.rplot': No such file or directory
rm: cannot remove `out.delta': No such file or directory

and additionally:

The tool produced the following additional output:
not exist the req png file!

For prokka I get for every file which is generated this error.

Fatal error: Exit code 2 ()
sh: 1: cannot open outdir/prokka.gbf: No such file
[08:53:49] Could not run command: sed 's/COORDINATES: profile/COORDINATES:profile/' < outdir\/prokka\.gbf > outdir\/prokka\.gbk

I thought that they are somehow related... Or not?

software error • 728 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by mschmid0
1

If you click on the bug icon it will give you additional information about the fail. Please share it with us.

ADD REPLYlink written 2.4 years ago by Martin Čech ♦♦ 4.5k
1

As Martin already said, we need more information. My guess is that your dependencies are not installed correctly and your tools do not produce the expected output.

ADD REPLYlink written 2.4 years ago by Bjoern Gruening5.0k
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