arahuja
commented
8 years ago Hi @ankushreddy - thanks for checking out Guacamole. Most of the callers are still in progress, but hopefully we can help you test them out. For germline-threshold, there is also a --threshold parameter to be aware of which is lowest VAF necessary to call a variant. It's unlikely you are hitting this, but just wanted to make you aware.
Does your BAM file have MDTags? If not, germline-threshold currently requires the reads already has mdtags, otherwise unfortunately, removes them. You can add mdtags through samtools or adam.
We do support computing of mdtags in Guacamole as well, but looking over the code, this isn't configured correctly right now. I wll file an issue for that and fix it.
ankushreddy
ryan-williams
Hi team,
When am submitting the job it is getting executed successfully but it is not calling any genotypes.
could you please help me with this issue.
please see the output of the spark-submit I have used.
16/01/27 16:14:02 INFO YarnScheduler: Adding task set 19.0 with 1 tasks 16/01/27 16:14:02 INFO TaskSetManager: Starting task 0.0 in stage 19.0 (TID 14, istb1-l2-b12-07.hadoop.priv, PROCESS_LOCAL, 1432 bytes) 16/01/27 16:14:02 INFO BlockManagerInfo: Added broadcast_15_piece0 in memory on istb1-l2-b12-07.hadoop.priv:38654 (size: 1808.0 B, free: 2.1 GB) 16/01/27 16:14:02 INFO DAGScheduler: Stage 19 (count at VariationRDDFunctions.scala:144) finished in 0.101 s 16/01/27 16:14:02 INFO TaskSetManager: Finished task 0.0 in stage 19.0 (TID 14) in 88 ms on istb1-l2-b12-07.hadoop.priv (1/1) 16/01/27 16:14:02 INFO YarnScheduler: Removed TaskSet 19.0, whose tasks have all completed, from pool 16/01/27 16:14:02 INFO DAGScheduler: Job 5 finished: count at VariationRDDFunctions.scala:144, took 0.115971 s 16/01/27 16:14:02 INFO VariantContextRDDFunctions: Write 0 records 16/01/27 16:14:02 INFO MapPartitionsRDD: Removing RDD 22 from persistence list 16/01/27 16:14:02 INFO BlockManager: Removing RDD 22 * Delayed Messages * Called 0 genotypes. Region counts: filtered 0 total regions to 0 relevant regions, expanded for overlaps by NaN% to 0 Regions per task: min=NaN 25%=NaN median=NaN (mean=NaN) 75%=NaN max=NaN. Max is NaN% more than mean. 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/metrics/json,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/stages/stage/kill,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/static,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/executors/threadDump/json,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/executors/threadDump,null} 16/01/27 16:14:03 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/executors/json,null}
Thanks & Regards, Ankush Reddy