Hi Johanna, This may be related to a prior known problem that I see in one of your parameters. Would you please share your history with me so that I can double check and provide feedback? Use the gear icon above the History pane and choose "Share or Publish", then click on the first button on the center form to generate the link, copy and email that back to me directly (not to the mailing list). Thanks for reporting the problem! Sorry for any confusion it caused, Jen Galaxy team On 10/11/13 12:23 AM, Johanna Sandgren wrote: > > Hi, > > I have this week used the new wrapper version of Cuffdiff that you > provide that should now include replicate information in output. But > there is no resulting files created. Why? I get all the results in > the right panel as usual and they are green (no error message) but > the they are all empty.. I use bam-files and cuffmerge files that I > have gotten result from before (both in spring and during summer- > when you upgraded cuffdiff version). I attach below info for one > resulting output. > > Kind regards, > > Johanna > > *Tool: Cuffdiff * > > Name: > > > > Cuffdiff on data 684, data 384, and others: transcript FPKM tracking > > Created: > > > > Oct 09, 2013 > > Filesize: > > > > 0 bytes > > Dbkey: > > > > hg19 > > Format: > > > > tabular > > Galaxy Tool Version: > > > > 0.0.6 > > Tool Version: > > > > cuffdiff v2.1.1 (4046M) > > Tool Standard Output: > > > > stdout > <https://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stdout> > > Tool Standard Error: > > > > stderr > <https://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stderr> > > Tool Exit Code: > > > > 0 > > API ID: > > > > bbd44e69cb8906b581bffe7ea9e0cd97 > > *Input Parameter* > > > > *Value* > > > > *Note for rerun* > > Transcripts > > > > 684: Cuffmerge on data 559, data 618, and others: merged transcripts > > > > Name > > > > MBs > > > > Add replicate > > > > 261: MarkDups_Dupes Marked s101_ok.bam > > > > Add replicate > > > > 348: s102_MarkDups_Dupes Marked on 256.bam > > > > Add replicate > > > > 412: s103MarkDups_Dupes Marked 357.bam > > > > Add replicate > > > > 378: s104MarkDups_Dupes Marked 347.bam > > > > Add replicate > > > > 425: s105MarkDups_Dupes Marked.bam > > > > Name > > > > Ctrls > > > > Add replicate > > > > 701: MarkDups_Dupes Marked688.bam > > > > Add replicate > > > > 671: SRR112675MarkDups_Dupes Marked417.bam > > > > Add replicate > > > > 433: SRR112673MarkDups_Dupes Marked 343.bam > > > > Add replicate > > > > 427: SRR111937MarkDups_Dupes Marked 376.bam > > > > Add replicate > > > > 382: SRR112601MarkDups_Dupes Marked 316.bam > > > > Add replicate > > > > 384: SRR111936MarkDups_Dupes Marked 328.bam > > > > Library normalization method > > > > geometric > > > > Dispersion estimation method > > > > pooled > > > > False Discovery Rate > > > > 0.05 > > > > Min Alignment Count > > > > 5 > > > > Use multi-read correct > > > > Yes > > > > Perform Bias Correction > > > > Yes > > > > Reference sequence data > > > > cached > > > > Include Read Group Datasets > > > > Yes > > > > Set Additional Parameters? (not recommended for paired-end reads) > > > > No > > > > ...................................................................................................................................................... > > Johanna Sandgren, PhD > > Department of Oncology-Pathology > > CCK, Karolinska Institutet > > SE-171 76 Stockholm, Sweden > > +46-8-517 721 35 (office), > > +46-8- 321047(fax), +46-708 388476 (mobile) > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/