[2020-02-06 18:31:19.836] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 18:31:19.836] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 18:31:19.836] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 18:31:19.836] [jointLog] [info] parsing read library format
[2020-02-06 18:31:19.836] [jointLog] [info] There is 1 library.
[2020-02-06 18:31:19.909] [jointLog] [info] Loading pufferfish index
[2020-02-06 18:31:19.910] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 18:31:20.720] [jointLog] [info] done
[2020-02-06 18:31:20.720] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 18:31:20.735] [jointLog] [info] Number of decoys : 0
[2020-02-06 18:31:36.643] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:31:36.649] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.652] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.654] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:31:36.656] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.664] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:31:36.680] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.682] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.685] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.686] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.692] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.692] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.693] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.713] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.715] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.717] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.720] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.733] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.734] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-06 18:31:36.737] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:31:36.738] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.744] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:31:36.748] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:31:36.748] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.749] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.750] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:31:36.913] [jointLog] [info] Computed 65,507 rich equivalence classes for further processing
[2020-02-06 18:31:36.913] [jointLog] [info] Counted 6,338,384 total reads in the equivalence classes 
[2020-02-06 18:31:36.925] [jointLog] [info] Number of mappings discarded because of alignment score : 662,064
[2020-02-06 18:31:36.925] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,215
[2020-02-06 18:31:36.925] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 18:31:36.925] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,664
[2020-02-06 18:31:36.925] [jointLog] [info] Mapping rate = 99.3519%

[2020-02-06 18:31:36.925] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 18:31:36.927] [jointLog] [info] Starting optimizer
[2020-02-06 18:31:36.942] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 18:31:36.945] [jointLog] [info] iteration = 0 | max rel diff. = 23265
[2020-02-06 18:31:36.914] [fileLog] [info] 
At end of round 0
==================
Observed 6379731 total fragments (6379731 in most recent round)

[2020-02-06 18:31:37.145] [jointLog] [info] iteration = 100 | max rel diff. = 1.70928
[2020-02-06 18:31:37.308] [jointLog] [info] iteration = 200 | max rel diff. = 2.65761
[2020-02-06 18:31:37.473] [jointLog] [info] iteration = 300 | max rel diff. = 2.22128
[2020-02-06 18:31:37.637] [jointLog] [info] iteration = 400 | max rel diff. = 1.24568
[2020-02-06 18:31:37.801] [jointLog] [info] iteration = 500 | max rel diff. = 0.0149694
[2020-02-06 18:31:37.964] [jointLog] [info] iteration = 600 | max rel diff. = 0.07431
[2020-02-06 18:31:38.128] [jointLog] [info] iteration = 700 | max rel diff. = 0.395179
[2020-02-06 18:31:38.292] [jointLog] [info] iteration = 800 | max rel diff. = 0.0252927
[2020-02-06 18:31:38.447] [jointLog] [info] iteration = 896 | max rel diff. = 0.00596524
[2020-02-06 18:31:38.448] [jointLog] [info] Finished optimizer
[2020-02-06 18:31:38.448] [jointLog] [info] writing output