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)



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