The MD5s for these tests were changed in commit 87435f1074615b2cd016f042980109fd53962c8d
to match the output of a broken version of BaseRecalibration. With the patch in
commit c397102ecc1fd1d2cd8f209a8f358ab4a60b50a7, the output once again matches the
*original* MD5s for these tests, and does not vary as you increase -nct.
Final resolution to GSA-632
-- Providing this optional argument -maxRuntime (in -maxRuntimeUnits units) causes the GATK to exit gracefully when the max. runtime has been exceeded. By cleanly I mean that the engine simply stops at the next available cycle in the walker as through the end of processing had been reached. This means that all output files are closed properly, etc.
-- Emits an info message that looks like "INFO 10:36:52,723 MicroScheduler - Aborting execution (cleanly) because the runtime has exceeded the requested maximum 10.0000 s". Otherwise there's currently no way to differentiate a truly completed run from a timelimit exceeded run, which may be a useful thing for a future update
-- Resolves GSA-630 / GATK max runtime to deal with bad LSA calling?
-- Added new JIRA entry for Ami to restart chr1 macarthur with this argument set to -maxRuntime 1 -maxRuntimeUnits DAYS to see if we can do all of chr1 in one weekend.
-- NCT wasn't previously recognized by Queue as needing more processors per machine. This commit fixes this. Also a potential cause of poor GATKPerformanceOverTime, in that runs with -nct could flood a node and cause it to have hundreds of cores in contention.
Caching and reusing ReadCovariates instances across reads sounds good in theory, but:
-it doesn't work unless you zero out the internal arrays before each read
-the internal arrays must be sized proportionally to the maximum POSSIBLE
recalibrated read length (5000!!!), instead of the ACTUAL read lengths
By contrast, creating a new instance per read is basically equivalent to doing an
efficient low-level memset-style clear on a much smaller array (since we use the actual
rather than the maximum read length to create it). So this should be faster than caching
instances and calling clear() but slower than caching instances and not calling clear().
Credit to Ryan to proposing this approach.
It turns out that pre-allocating the entire tree was too expensive in
terms of memory when using large values for the -mcs and -ics parameters.
Pre-allocating the first two dimensions prevents us from ever locking the
root node during a put(). Contention between threads over lower levels
of the tree should be minimal given that puts are rare compared to gets.
Also output dimensions and pre-allocation info at startup. If pre-allocation
takes longer than usual this gives the user a sense of what is causing the
delay.
-- I'm committing because there's some kind of fundamental problem with the ReadCovariates cache, in that historical data isn't being cleared / computed properly, and I'd rather it fail for a while than leave it in JIRA.
-- The integration tests test the -nct with PrintReads to get 1, 2, 4 and the 4 fails. But that's because of this incorrect calculation
-- Updating GATKPerformanceOverTime with the new @ClassType annotation
a) Connect picard outputs with @Output
b) Do QC by default and correct picard path in instances.
c) EXPERIMENTAL: bump up numThreads to 8 by default and see what happens
DEV-155 #resolve #time 1m
kshakir
Kristian Cibulskis
Guillermo del Angel
Mauricio Carneiro
Andrey Sivachenko
Mark DePristo
Eric Banks
Ryan Poplin
David Roazen
Yossi Farjoun
Ami Levy Moonshine
Scott Frazer