[2020-02-07 08:27:46.851] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 08:27:46.851] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 08:27:46.851] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 08:27:46.851] [jointLog] [info] parsing read library format
[2020-02-07 08:27:46.851] [jointLog] [info] There is 1 library.
[2020-02-07 08:27:46.929] [jointLog] [info] Loading pufferfish index
[2020-02-07 08:27:46.929] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 08:27:47.845] [jointLog] [info] done
[2020-02-07 08:27:47.845] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 08:27:47.862] [jointLog] [info] Number of decoys : 0
[2020-02-07 08:28:03.694] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.695] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.697] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.705] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:28:03.715] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:28:03.720] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.723] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.727] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.728] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.729] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.730] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.732] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 08:28:03.733] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments
[2020-02-07 08:28:03.754] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.760] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 08:28:03.763] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.767] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.769] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.772] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.774] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:28:03.775] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.776] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.779] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.782] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:28:03.785] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.790] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:28:03.791] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:28:03.915] [jointLog] [info] Computed 59,790 rich equivalence classes for further processing
[2020-02-07 08:28:03.915] [jointLog] [info] Counted 6,001,678 total reads in the equivalence classes 
[2020-02-07 08:28:03.929] [jointLog] [info] Number of mappings discarded because of alignment score : 579,980
[2020-02-07 08:28:03.929] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,873
[2020-02-07 08:28:03.929] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 08:28:03.929] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,286
[2020-02-07 08:28:03.929] [jointLog] [info] Mapping rate = 99.4934%

[2020-02-07 08:28:03.929] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 08:28:03.930] [jointLog] [info] Starting optimizer
[2020-02-07 08:28:03.948] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 08:28:03.951] [jointLog] [info] iteration = 0 | max rel diff. = 22295.9
[2020-02-07 08:28:03.916] [fileLog] [info] 
At end of round 0
==================
Observed 6032238 total fragments (6032238 in most recent round)

[2020-02-07 08:28:04.144] [jointLog] [info] iteration = 100 | max rel diff. = 13.372
[2020-02-07 08:28:04.323] [jointLog] [info] iteration = 200 | max rel diff. = 0.639066
[2020-02-07 08:28:04.502] [jointLog] [info] iteration = 300 | max rel diff. = 0.796703
[2020-02-07 08:28:04.681] [jointLog] [info] iteration = 400 | max rel diff. = 0.849673
[2020-02-07 08:28:04.860] [jointLog] [info] iteration = 500 | max rel diff. = 0.577658
[2020-02-07 08:28:05.040] [jointLog] [info] iteration = 600 | max rel diff. = 1.20647
[2020-02-07 08:28:05.219] [jointLog] [info] iteration = 700 | max rel diff. = 0.0478911
[2020-02-07 08:28:05.397] [jointLog] [info] iteration = 800 | max rel diff. = 0.108869
[2020-02-07 08:28:05.567] [jointLog] [info] iteration = 896 | max rel diff. = 0.00850599
[2020-02-07 08:28:05.568] [jointLog] [info] Finished optimizer
[2020-02-07 08:28:05.568] [jointLog] [info] writing output