[2020-02-07 11:04:27.811] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 11:04:27.811] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 11:04:27.811] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 11:04:27.811] [jointLog] [info] parsing read library format
[2020-02-07 11:04:27.811] [jointLog] [info] There is 1 library.
[2020-02-07 11:04:27.886] [jointLog] [info] Loading pufferfish index
[2020-02-07 11:04:27.886] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 11:04:28.394] [jointLog] [info] done
[2020-02-07 11:04:28.394] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 11:04:28.411] [jointLog] [info] Number of decoys : 0
[2020-02-07 11:04:47.192] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.196] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.211] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 11:04:47.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 11:04:47.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.227] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.235] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.239] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.240] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.240] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 11:04:47.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-07 11:04:47.246] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.256] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.261] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.264] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.272] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.272] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.273] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.283] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.285] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:04:47.287] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.287] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.288] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.291] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:04:47.422] [jointLog] [info] Computed 65,587 rich equivalence classes for further processing
[2020-02-07 11:04:47.422] [jointLog] [info] Counted 6,338,368 total reads in the equivalence classes 
[2020-02-07 11:04:47.437] [jointLog] [info] Number of mappings discarded because of alignment score : 662,619
[2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,232
[2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,659
[2020-02-07 11:04:47.437] [jointLog] [info] Mapping rate = 99.3516%

[2020-02-07 11:04:47.437] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 11:04:47.437] [jointLog] [info] Starting optimizer
[2020-02-07 11:04:47.455] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 11:04:47.457] [jointLog] [info] iteration = 0 | max rel diff. = 23273.5
[2020-02-07 11:04:47.423] [fileLog] [info] 
At end of round 0
==================
Observed 6379731 total fragments (6379731 in most recent round)

[2020-02-07 11:04:47.631] [jointLog] [info] iteration = 100 | max rel diff. = 1.94389
[2020-02-07 11:04:47.793] [jointLog] [info] iteration = 200 | max rel diff. = 12.3524
[2020-02-07 11:04:47.955] [jointLog] [info] iteration = 300 | max rel diff. = 10.4115
[2020-02-07 11:04:48.117] [jointLog] [info] iteration = 400 | max rel diff. = 0.139701
[2020-02-07 11:04:48.279] [jointLog] [info] iteration = 500 | max rel diff. = 0.0372542
[2020-02-07 11:04:48.443] [jointLog] [info] iteration = 600 | max rel diff. = 0.0634977
[2020-02-07 11:04:48.604] [jointLog] [info] iteration = 700 | max rel diff. = 0.358358
[2020-02-07 11:04:48.653] [jointLog] [info] iteration = 731 | max rel diff. = 0.0071866
[2020-02-07 11:04:48.653] [jointLog] [info] Finished optimizer
[2020-02-07 11:04:48.653] [jointLog] [info] writing output