[2020-02-06 21:03:01.729] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 21:03:01.729] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 21:03:01.729] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 21:03:01.729] [jointLog] [info] parsing read library format
[2020-02-06 21:03:01.729] [jointLog] [info] There is 1 library.
[2020-02-06 21:03:01.815] [jointLog] [info] Loading pufferfish index
[2020-02-06 21:03:01.816] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 21:03:02.495] [jointLog] [info] done
[2020-02-06 21:03:02.495] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 21:03:02.510] [jointLog] [info] Number of decoys : 0
[2020-02-06 21:03:20.749] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:03:20.755] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:03:20.755] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.776] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.778] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.779] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.779] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.780] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.788] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.790] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.793] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.808] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-06 21:03:20.812] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.815] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.816] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.818] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 21:03:20.829] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.829] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.837] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.844] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.846] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:20.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:03:20.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:03:21.029] [jointLog] [info] Computed 65,558 rich equivalence classes for further processing
[2020-02-06 21:03:21.029] [jointLog] [info] Counted 6,338,387 total reads in the equivalence classes 
[2020-02-06 21:03:21.044] [jointLog] [info] Number of mappings discarded because of alignment score : 661,936
[2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,217
[2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,669
[2020-02-06 21:03:21.044] [jointLog] [info] Mapping rate = 99.3519%

[2020-02-06 21:03:21.044] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 21:03:21.045] [jointLog] [info] Starting optimizer
[2020-02-06 21:03:21.062] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 21:03:21.065] [jointLog] [info] iteration = 0 | max rel diff. = 23262.4
[2020-02-06 21:03:21.266] [jointLog] [info] iteration = 100 | max rel diff. = 4.47073
[2020-02-06 21:03:21.030] [fileLog] [info] 
At end of round 0
==================
Observed 6379731 total fragments (6379731 in most recent round)

[2020-02-06 21:03:21.434] [jointLog] [info] iteration = 200 | max rel diff. = 9.41736
[2020-02-06 21:03:21.603] [jointLog] [info] iteration = 300 | max rel diff. = 2.37717
[2020-02-06 21:03:21.772] [jointLog] [info] iteration = 400 | max rel diff. = 0.428437
[2020-02-06 21:03:21.940] [jointLog] [info] iteration = 500 | max rel diff. = 0.0680179
[2020-02-06 21:03:22.108] [jointLog] [info] iteration = 600 | max rel diff. = 0.125135
[2020-02-06 21:03:22.276] [jointLog] [info] iteration = 700 | max rel diff. = 0.662162
[2020-02-06 21:03:22.281] [jointLog] [info] iteration = 704 | max rel diff. = 0.00650071
[2020-02-06 21:03:22.282] [jointLog] [info] Finished optimizer
[2020-02-06 21:03:22.282] [jointLog] [info] writing output