no error and no output from cuffcompare

[hibachings2013]

Dear Guys,

I just ran cuffcompare, but no output and no errors.

Here is my command for cuffcompare

./cuffcompare -o /Users/puruna/cuffcompare_output/s1 -R -r /Users/puruna/reference.gtf -s /Users/puruna/transcripts_s1.gtf

And if i use this command

./cuffcompare -o cuffcompare -r /Users/puruna/ref.gtf /Users/puruna/cufflinks_output/transcripts_s1.gtf

then, i got only two output files with .tmap and .refmap, NO .stats, NO tracking, NO combined.gtf

I don't know what is wrong. I would greatly appreciate any feedback from this community!

[arkfang]

Because you gave a output directory while cuffcompare asked for a output prefix. Which means you give a blank prefix to cuffcompare.
So the outputs that are supposed to be output_prefix.combined.gtf are now just .combined.gtf.
And in a lot of linux-like systems, .* file (a file starts with dot) is treated as a hidden file.
Check your output directory and you probably will see them there, hidden.