Hello! I've been working on developing a QC and filtering pipeline for UKB exome data using Hail on JupyterLab. For the past two operations I've tried to run, I've received a "ConnectionPoolTimeoutException: Timeout waiting for connection from pool" error (full error trace attached) after waiting for about 15 minutes for a command to finish executing (this is about how long I would've expected the commands to take had they completed successfully). The first time was when I tried to summarize a Hail table, and the second was when I tried to write a Hail table to a DNAX database. I'm not sure where this error is coming from or how to fix it. I'm working on a high priority mem2_ssd1_v2_x16 instance, and I'm not even close to encroaching on my memory limitations:
CPU: 0% (16 cores) * Memory: 14100/62846MB * Storage: 519GB free * Net: 0?/0?MBps
Is this an issue with my job/DNAnexus, or is it something that may be more related to Hail? Thanks!
Is this error reproducible with smaller data size?
Is this behavior reproducible with different instance type (let's say larger memory one, such as mem3)? What if you select a higher number of computing nodes?
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3 comments
+ you'd need to provide a code sample
@Lara Brown? we can't do much without seeing log of the job. I recommend that you contact ukbiobank-support@dnanexus.com for help.
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