[2020-04-26 02:39:56.262] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 02:39:56.262] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 02:39:56.262] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 02:39:56.262] [jointLog] [info] parsing read library format
[2020-04-26 02:39:56.262] [jointLog] [info] There is 1 library.
[2020-04-26 02:39:56.315] [jointLog] [info] Loading pufferfish index
[2020-04-26 02:39:56.315] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 02:39:56.508] [jointLog] [info] done
[2020-04-26 02:39:56.508] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 02:39:56.520] [jointLog] [info] Number of decoys : 0
[2020-04-26 02:40:03.431] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-26 02:40:03.430] [jointLog] [info] Computed 76,366 rich equivalence classes for further processing
[2020-04-26 02:40:03.430] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes 
[2020-04-26 02:40:03.448] [jointLog] [info] Number of mappings discarded because of alignment score : 536,822
[2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061
[2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328
[2020-04-26 02:40:03.451] [jointLog] [warning] Only 2319185 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 02:40:03.451] [jointLog] [info] Mapping rate = 99.1791%

[2020-04-26 02:40:03.451] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 02:40:03.452] [jointLog] [info] Starting optimizer
[2020-04-26 02:40:03.474] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 02:40:03.479] [jointLog] [info] iteration = 0 | max rel diff. = 4684.72
[2020-04-26 02:40:03.767] [jointLog] [info] iteration = 100 | max rel diff. = 4.44958
[2020-04-26 02:40:04.049] [jointLog] [info] iteration = 200 | max rel diff. = 5.04084
[2020-04-26 02:40:04.332] [jointLog] [info] iteration = 300 | max rel diff. = 0.57508
[2020-04-26 02:40:04.617] [jointLog] [info] iteration = 400 | max rel diff. = 0.247405
[2020-04-26 02:40:04.896] [jointLog] [info] iteration = 500 | max rel diff. = 0.034264
[2020-04-26 02:40:05.173] [jointLog] [info] iteration = 600 | max rel diff. = 0.0973451
[2020-04-26 02:40:05.461] [jointLog] [info] iteration = 700 | max rel diff. = 0.0636478
[2020-04-26 02:40:05.746] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262892
[2020-04-26 02:40:06.032] [jointLog] [info] iteration = 900 | max rel diff. = 0.0158562
[2020-04-26 02:40:06.316] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0172616
[2020-04-26 02:40:06.490] [jointLog] [info] iteration = 1,062 | max rel diff. = 0.00190054
[2020-04-26 02:40:06.491] [jointLog] [info] Finished optimizer
[2020-04-26 02:40:06.491] [jointLog] [info] writing output