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
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
The Cloudmap pipeline has several tools with dependency issues.
Please follow progress for the correction here: (the tool author is involved in troubleshooting)
All open issues reported by users can be tracked here:
Thanks for your patience during the upgrade at http://usegalaxy.org, Jen, Galaxy team
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