[2020-02-06 18:57:47.663] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 18:57:47.663] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 18:57:47.663] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 18:57:47.663] [jointLog] [info] parsing read library format
[2020-02-06 18:57:47.663] [jointLog] [info] There is 1 library.
[2020-02-06 18:57:47.727] [jointLog] [info] Loading pufferfish index
[2020-02-06 18:57:47.727] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 18:57:47.797] [jointLog] [info] done
[2020-02-06 18:57:47.797] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 18:57:47.806] [jointLog] [info] Number of decoys : 0
[2020-02-06 18:58:06.682] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.683] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.687] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:58:06.690] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.696] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.697] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.704] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:58:06.709] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.719] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:58:06.719] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:58:06.725] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.729] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.747] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.767] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.769] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:58:06.791] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.792] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.793] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.798] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:58:06.798] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.799] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.801] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:58:06.803] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.805] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.806] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.806] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:58:06.807] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:58:06.808] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:58:06.931] [jointLog] [info] Computed 56,062 rich equivalence classes for further processing
[2020-02-06 18:58:06.931] [jointLog] [info] Counted 6,861,116 total reads in the equivalence classes 
[2020-02-06 18:58:06.946] [jointLog] [info] Number of mappings discarded because of alignment score : 914,860
[2020-02-06 18:58:06.946] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,632
[2020-02-06 18:58:06.946] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 18:58:06.946] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,057
[2020-02-06 18:58:06.946] [jointLog] [info] Mapping rate = 99.5863%

[2020-02-06 18:58:06.946] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 18:58:06.947] [jointLog] [info] Starting optimizer
[2020-02-06 18:58:06.963] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 18:58:06.967] [jointLog] [info] iteration = 0 | max rel diff. = 29778.1
[2020-02-06 18:58:06.931] [fileLog] [info] 
At end of round 0
==================
Observed 6889615 total fragments (6889615 in most recent round)

[2020-02-06 18:58:07.238] [jointLog] [info] iteration = 100 | max rel diff. = 16.0161
[2020-02-06 18:58:07.469] [jointLog] [info] iteration = 200 | max rel diff. = 1.83559
[2020-02-06 18:58:07.700] [jointLog] [info] iteration = 300 | max rel diff. = 0.437975
[2020-02-06 18:58:07.928] [jointLog] [info] iteration = 400 | max rel diff. = 0.0285139
[2020-02-06 18:58:08.159] [jointLog] [info] iteration = 500 | max rel diff. = 0.364312
[2020-02-06 18:58:08.388] [jointLog] [info] iteration = 600 | max rel diff. = 0.0599725
[2020-02-06 18:58:08.619] [jointLog] [info] iteration = 700 | max rel diff. = 0.034152
[2020-02-06 18:58:08.690] [jointLog] [info] iteration = 732 | max rel diff. = 0.00510688
[2020-02-06 18:58:08.690] [jointLog] [info] Finished optimizer
[2020-02-06 18:58:08.690] [jointLog] [info] writing output