My lab has previously used the CloudMap pipeline to identify the location of mutations from in C. elegans strains using the "CloudMap Hawaiian Variant Mapping with WGS and Variant Calling" workflow. However, our most recent batch of analyses has run into an issue. When we run the data the workflow stops at the "Realigner Target Creator (GATK intervals)”, with a tool error: “failure preparing job”.
I initially thought that maybe there was something wrong with our imported workflow, so I reimported the CloudMap workflow, and ran the analysis again, getting the same error. Same results with a dataset from one of our other mutants.
Finally, I imported the ot266 'proof-of-principle" dataset and ran the analysis again. Same error. I have now tried this analysis with all available CloudMap workflows on the Galaxy main server and always get the same error at Realigner Target Creator (GATK intervals). I can only conclude that there is some issue with the GATK tool on the main public instance of Galaxy.
Can anyone suggest a remedy? I am using the datasets associated with CloudMap on the main Galaxy server and these have work up until this latest batch.