[2020-02-07 05:48:14.915] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 05:48:14.915] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 05:48:14.915] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 05:48:14.915] [jointLog] [info] parsing read library format
[2020-02-07 05:48:14.916] [jointLog] [info] There is 1 library.
[2020-02-07 05:48:14.992] [jointLog] [info] Loading pufferfish index
[2020-02-07 05:48:15.004] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 05:48:15.664] [jointLog] [info] done
[2020-02-07 05:48:15.665] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 05:48:15.682] [jointLog] [info] Number of decoys : 0
[2020-02-07 05:48:33.301] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.302] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.307] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.318] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.319] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.334] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.342] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.342] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.343] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 05:48:33.350] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.356] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.357] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.366] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.370] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.374] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.379] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.391] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.393] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 05:48:33.393] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.396] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.400] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.404] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.408] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 05:48:33.411] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 05:48:33.533] [jointLog] [info] Computed 65,439 rich equivalence classes for further processing
[2020-02-07 05:48:33.533] [jointLog] [info] Counted 6,338,345 total reads in the equivalence classes 
[2020-02-07 05:48:33.547] [jointLog] [info] Number of mappings discarded because of alignment score : 662,283
[2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,252
[2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,647
[2020-02-07 05:48:33.547] [jointLog] [info] Mapping rate = 99.3513%

[2020-02-07 05:48:33.547] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 05:48:33.548] [jointLog] [info] Starting optimizer
[2020-02-07 05:48:33.565] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 05:48:33.567] [jointLog] [info] iteration = 0 | max rel diff. = 23254.5
[2020-02-07 05:48:33.534] [fileLog] [info] 
At end of round 0
==================
Observed 6379731 total fragments (6379731 in most recent round)

[2020-02-07 05:48:33.735] [jointLog] [info] iteration = 100 | max rel diff. = 6.12481
[2020-02-07 05:48:33.891] [jointLog] [info] iteration = 200 | max rel diff. = 1.62517
[2020-02-07 05:48:34.047] [jointLog] [info] iteration = 300 | max rel diff. = 10.8648
[2020-02-07 05:48:34.204] [jointLog] [info] iteration = 400 | max rel diff. = 0.250715
[2020-02-07 05:48:34.360] [jointLog] [info] iteration = 500 | max rel diff. = 0.084418
[2020-02-07 05:48:34.516] [jointLog] [info] iteration = 600 | max rel diff. = 0.174293
[2020-02-07 05:48:34.673] [jointLog] [info] iteration = 700 | max rel diff. = 0.0544346
[2020-02-07 05:48:34.831] [jointLog] [info] iteration = 800 | max rel diff. = 0.0330384
[2020-02-07 05:48:34.987] [jointLog] [info] iteration = 900 | max rel diff. = 0.0371923
[2020-02-07 05:48:35.032] [jointLog] [info] iteration = 930 | max rel diff. = 0.00789576
[2020-02-07 05:48:35.033] [jointLog] [info] Finished optimizer
[2020-02-07 05:48:35.033] [jointLog] [info] writing output