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)
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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
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)
___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
-- 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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
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Jennifer Jackson -
Johanna Sandgren