Question: Problem with cloudmap workflow
1
gravatar for husthwm
21 months ago by
husthwm30
husthwm30 wrote:

Hi I am using cloudmap workflow on Galaxy main sever to identify the mutation of mutant C. elegans. When I ran ' Hawaiian and Variant Discovery Mapping on Hawaiian Mapped Samples (and Variant Calling) workflow _2-7-2014' workflow, the process stopped at step 6. Does anyone know what is going on? The following is the link of my history: https://usegalaxy.org/u/wenming789/h/dimported-cloudmap-hawaiian-and-variant-discovery-mapping-on-hawaiian-mapped-samples-and-variant-calling-workflow-2-7-2014 Best Wenm

software error • 582 views
ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson23k • written 21 months ago by husthwm30

FastQC was problematic since later yesterday. The tool is undergoing correction. We will reply once this is done. Thank you for your patience, Jen, Galaxy team

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson23k
1
gravatar for husthwm
21 months ago by
husthwm30
husthwm30 wrote:

Hi Jen,

Thanks for your reply. FasQC works quite well now. However, when I ran the workflow again, it stopped at the step "Map with BWA for Illumina" .

Could you please have a look? Here is the history link: https://usegalaxy.org/u/wenming789/h/dimported-cloudmap-hawaiian-and-variant-discovery-mapping-on-hawaiian-mapped-samples-and-variant-calling-workflow-2-7-2014-1

Best

Wenming

ADD COMMENTlink written 21 months ago by husthwm30

Thanks, I am reviewing and will get back to you shortly. There was a small problem with importing histories last night, but I expect that to be corrected soon. Galaxy Main is undergoing significant upgrades at this time (as noted in the top banner at http://usegalaxy.org), but we are working to get the server back up and going, even better than ever! Jen

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson23k

Hi Jen, Here are some updates for the problems with the workflow "CloudMap Hawaiian and Variant Discovery Mapping on Hawaiian Mapped Samples": I ran the it again and this time the step "Map with BWA for Illumina" was fine. However, the workflow stopped at the step "Select Variants on data 34, data 5, and data 39 (Variant File)" Here is the link:
https://usegalaxy.org/u/wenming789/h/a-imported-cloudmap-hawaiian-and-variant-discovery-mapping-on-hawaiian-mapped-samples-and-variant-calling-workflow-2-7-2014

Best

Wenming

ADD REPLYlink written 21 months ago by husthwm30
1
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson23k wrote:

The Cloudmap pipeline has several tools with dependency issues.

Please follow progress for the correction here: (the tool author is involved in troubleshooting)

https://github.com/galaxyproject/galaxy/issues/2304

All open issues reported by users can be tracked here:

https://github.com/jennaj/support-known-issues/wiki

Thanks for your patience during the upgrade at http://usegalaxy.org, Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

FastQC is now functional again at http://usegalaxy.org. Thanks for reporting the problem.

Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson23k

Hi Jen,

Thanks for your reply. FasQC works quite well now. However, when I ran the workflow again, it stopped at the step "Map with BWA for Illumina" .

Could you please have a look? Here is the history link: https://usegalaxy.org/u/wenming789/h/dimported-cloudmap-hawaiian-and-variant-discovery-mapping-on-hawaiian-mapped-samples-and-variant-calling-workflow-2-7-2014-1

Best

Wenming

ADD REPLYlink written 21 months ago by husthwm30
0
gravatar for Felix Mayr
20 months ago by
Felix Mayr10
Germany
Felix Mayr10 wrote:

Hi all,

I would like to report the problem I encounter running the Hawaiian SNP mapping workflow (same as used by Wenming).

The workflow works fine until the point it tries to draw the curves needed for the mapping. I get the following error:


51 CloudMap: Hawaiian Variant Mapping with WGS data on data 39 error An error occurred with this dataset: Error in lines(loess.smooth(x, y, span = 0.1), lwd = 5, col = "red") : could not find function "loess.smooth"

There was an error creating the location plot pdf... Please try again Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load sh


Here is the link to my workflow: https://usegalaxy.org/u/felixams/h/dh803

Is the loess.smooth function still properly installed?

All best, Felix

ADD COMMENTlink written 20 months ago by Felix Mayr10

Hi Felix, here's your data replotted on our MiModD NacreousMap server => http://mapping-by-sequencing.vm.uni-freiburg.de:8080/u/wolma/h/felix. See my answer to Wenming in this related post for more information. Best, Wolfgang

ADD REPLYlink modified 20 months ago • written 20 months ago by Wolfgang Maier390
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