[2020-02-07 06:14:43.364] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 06:14:43.364] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 06:14:43.364] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 06:14:43.364] [jointLog] [info] parsing read library format
[2020-02-07 06:14:43.364] [jointLog] [info] There is 1 library.
[2020-02-07 06:14:43.443] [jointLog] [info] Loading pufferfish index
[2020-02-07 06:14:43.443] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 06:14:43.540] [jointLog] [info] done
[2020-02-07 06:14:43.540] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 06:14:43.549] [jointLog] [info] Number of decoys : 0
[2020-02-07 06:15:02.229] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.234] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:15:02.243] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.251] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.258] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.265] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.274] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.282] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:15:02.282] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.297] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:15:02.314] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.319] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:15:02.326] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.331] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:15:02.335] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:15:02.347] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.348] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.353] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.356] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:15:02.358] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:15:02.473] [jointLog] [info] Computed 56,040 rich equivalence classes for further processing
[2020-02-07 06:15:02.473] [jointLog] [info] Counted 6,861,144 total reads in the equivalence classes 
[2020-02-07 06:15:02.489] [jointLog] [info] Number of mappings discarded because of alignment score : 914,422
[2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,608
[2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,055
[2020-02-07 06:15:02.489] [jointLog] [info] Mapping rate = 99.5868%

[2020-02-07 06:15:02.489] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 06:15:02.490] [jointLog] [info] Starting optimizer
[2020-02-07 06:15:02.509] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 06:15:02.512] [jointLog] [info] iteration = 0 | max rel diff. = 29792.4
[2020-02-07 06:15:02.474] [fileLog] [info] 
At end of round 0
==================
Observed 6889615 total fragments (6889615 in most recent round)

[2020-02-07 06:15:02.758] [jointLog] [info] iteration = 100 | max rel diff. = 3.57875
[2020-02-07 06:15:02.987] [jointLog] [info] iteration = 200 | max rel diff. = 0.389661
[2020-02-07 06:15:03.214] [jointLog] [info] iteration = 300 | max rel diff. = 0.421193
[2020-02-07 06:15:03.442] [jointLog] [info] iteration = 400 | max rel diff. = 0.126702
[2020-02-07 06:15:03.670] [jointLog] [info] iteration = 500 | max rel diff. = 0.367529
[2020-02-07 06:15:03.899] [jointLog] [info] iteration = 600 | max rel diff. = 0.132982
[2020-02-07 06:15:04.126] [jointLog] [info] iteration = 700 | max rel diff. = 0.0901902
[2020-02-07 06:15:04.231] [jointLog] [info] iteration = 747 | max rel diff. = 0.00660845
[2020-02-07 06:15:04.231] [jointLog] [info] Finished optimizer
[2020-02-07 06:15:04.231] [jointLog] [info] writing output