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.

Sparks tool TaskMemoryManager WARN

Using ApplyBQSRSpark I experienced the following WARN and it stopped. There were more than 60 GB of RAM free on the server I used at that time, and every time I lauch the command it gives the same output. This is the command that I run using docker:

/gatk/gatk ApplyBQSRSpark \
-I ${INPUT_FILE_BAM} \
--bqsr-recal-file recal_data_.table \
-O /BQSRS_.bam

18/06/13 10:51:15 INFO BlockManagerInfo: Removed broadcast_2_piece0 on 172.17.0.2:44253 in memory (size: 5.7 KB, free: 15.8 GB)
18/06/13 11:04:55 WARN TaskMemoryManager: Failed to allocate a page (8388608 bytes), try again.
18/06/13 11:06:32 WARN NettyRpcEnv: Ignored message: HeartbeatResponse(false)
18/06/13 11:08:03 WARN TaskMemoryManager: Failed to allocate a page (8388608 bytes), try again.
18/06/13 11:09:51 WARN TaskMemoryManager: Failed to allocate a page (8388608 bytes), try again.

Tagged:

Best Answer

Answers

Sign In or Register to comment.