Problem with cloudmap workflow

Question: Problem with cloudmap workflow

2.6 years ago by

husthwm • 30 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 • 1.0k views

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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by husthwm • 30

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 REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

husthwm • 30

husthwm • 30 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 COMMENT • link written 2.6 years ago by husthwm • 30

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 REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.6 years ago by husthwm • 30

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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" .

Best

Wenming

ADD REPLY • link written 2.6 years ago by husthwm • 30

2.6 years ago by

Felix Mayr • 10

Germany

Felix Mayr • 10 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 COMMENT • link written 2.6 years ago by Felix Mayr • 10

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 REPLY • link modified 2.5 years ago • written 2.5 years ago by Wolfgang Maier • 600

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