Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
CNVDiscovery pipeline no ".done" file ?
In the CNVDiscovery pipeline working directory "cnv_stage2", seq_chr2 always restart all the jobs when I redo the pipeline, unlike other chromosomes. I checked the seq_chr2 folder, even though I could see all the P0xxx.genotypes.. files, there are no ".done" file at all. I could find the ".done" files in other chromosome folders. I wonder if there is bug peculiar to chromosome 2 in stage 2? Or ".done" files are all produced at once at the very end for each chromosome? (This seems unlikely, as the progress seems stuck, as the log shows that
INFO 13:02:52,137 QGraph - 8 Pend, 456 Run, 0 Fail, 0 Done
after 3 days running, but I could see all the 456 partitions' files in the seq_chr2 folder.)
I wonder if I could just use
to mark these partitions as "done"?