Cuffcompare - no output, no warnings

[bruce01]

Hi,

I am running cuffcompare after making transcripts.gtf and merging those for each of the two conditions I wish to investigate. I am running without a gtf reference (I want to see the difference between running with and without -g ref.gtf makes). I am using cuffcompare 2.0.0:

cuffcompare -o ~/cufflinks/cuffComp/no_gtf/ -V -s /data/ref.gtf
/cufflinks/N_merged.cufflink_no_gtf/transcripts.gtf
/cufflinks/P_merged.cufflink_no_gtf/transcripts.gtf

I get no output at all. Verbose gives me the following:

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Prefix for output files:
Processing qfile #1: /cufflinks/N_merged.cufflink_no_gtf/merged.gtf
Loading transcripts from /cufflinks/N_merged.cufflink_no_gtf/merged.gtf..
Processing qfile #2: /cufflinks/P_merged.cufflink_no_gtf/merged.gtf
Loading transcripts from /cufflinks/P_merged.cufflink_no_gtf/merged.gtf..
Tracking transcripts across 2 query files..
Cleaning up..
Done.

This takes ~30 seconds. Tried with transcripts.gtf also. Also tried with another set of gtf files. Running with a ref.gtf gives:

<list of duplicates>
61 duplicate reference transcripts discarded.
..reference annotation loaded
Prefix for output files:
Processing qfile #1: /cufflinks/N_merged.cufflink_gtf/merged.gtf
Loading transcripts from /cufflinks/N_merged.cufflink_gtf/merged.gtf..
2134 redundant cufflinks transfrags discarded.
Found 11538 transcripts with undetermined strand.
Processing qfile #2: /cufflinks/P_merged.cufflink_gtf/merged.gtf
Loading transcripts from /cufflinks/P_merged.cufflink_gtf/merged.gtf..
1145 redundant cufflinks transfrags discarded.
Found 11302 transcripts with undetermined strand.
Tracking transcripts across 2 query files..
Cleaning up..
Done.


Any advice or help would be very much appreciated

[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.