[2020-02-07 06:38:35.171] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 06:38:35.171] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 06:38:35.171] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 06:38:35.171] [jointLog] [info] parsing read library format
[2020-02-07 06:38:35.171] [jointLog] [info] There is 1 library.
[2020-02-07 06:38:35.248] [jointLog] [info] Loading pufferfish index
[2020-02-07 06:38:35.249] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 06:38:35.949] [jointLog] [info] done
[2020-02-07 06:38:35.949] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 06:38:35.966] [jointLog] [info] Number of decoys : 0
[2020-02-07 06:38:52.806] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.807] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.809] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.812] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.817] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.820] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.825] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:38:52.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.852] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.858] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.870] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.882] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.883] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.890] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.896] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.904] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:38:52.907] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.916] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:52.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:38:52.919] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:38:52.919] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:38:52.920] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:38:52.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:38:53.048] [jointLog] [info] Computed 55,920 rich equivalence classes for further processing
[2020-02-07 06:38:53.048] [jointLog] [info] Counted 6,861,138 total reads in the equivalence classes 
[2020-02-07 06:38:53.064] [jointLog] [info] Number of mappings discarded because of alignment score : 914,634
[2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,613
[2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,043
[2020-02-07 06:38:53.065] [jointLog] [info] Mapping rate = 99.5867%

[2020-02-07 06:38:53.065] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 06:38:53.066] [jointLog] [info] Starting optimizer
[2020-02-07 06:38:53.083] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 06:38:53.086] [jointLog] [info] iteration = 0 | max rel diff. = 29797.6
[2020-02-07 06:38:53.337] [jointLog] [info] iteration = 100 | max rel diff. = 4.72741
[2020-02-07 06:38:53.049] [fileLog] [info] 
At end of round 0
==================
Observed 6889615 total fragments (6889615 in most recent round)

[2020-02-07 06:38:53.574] [jointLog] [info] iteration = 200 | max rel diff. = 0.527137
[2020-02-07 06:38:53.811] [jointLog] [info] iteration = 300 | max rel diff. = 1.27619
[2020-02-07 06:38:54.048] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284666
[2020-02-07 06:38:54.284] [jointLog] [info] iteration = 500 | max rel diff. = 0.358911
[2020-02-07 06:38:54.521] [jointLog] [info] iteration = 600 | max rel diff. = 0.0455363
[2020-02-07 06:38:54.756] [jointLog] [info] iteration = 700 | max rel diff. = 0.0317149
[2020-02-07 06:38:54.840] [jointLog] [info] iteration = 736 | max rel diff. = 0.0054179
[2020-02-07 06:38:54.841] [jointLog] [info] Finished optimizer
[2020-02-07 06:38:54.841] [jointLog] [info] writing output