Hi again,
I am also going to recommend that you just go ahead and re-run the job
to see if that clears up the issue. Some new testing indicates that the
prior issue is now cleared - and this will get you back to work the
quickest.
Best,
Jen
Galaxy team
On 10/11/13 2:23 PM, Jennifer Jackson wrote:
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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http://galaxyproject.org
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