[2020-02-07 06:05:52.932] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 06:05:52.932] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 06:05:52.932] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 06:05:52.932] [jointLog] [info] parsing read library format
[2020-02-07 06:05:52.932] [jointLog] [info] There is 1 library.
[2020-02-07 06:05:53.008] [jointLog] [info] Loading pufferfish index
[2020-02-07 06:05:53.008] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 06:05:53.246] [jointLog] [info] done
[2020-02-07 06:05:53.246] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 06:05:53.263] [jointLog] [info] Number of decoys : 0
[2020-02-07 06:06:11.710] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.715] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:06:11.716] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.729] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.732] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.736] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:06:11.741] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.742] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.743] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.744] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.761] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments
[2020-02-07 06:06:11.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:06:11.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:06:11.809] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:06:11.810] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.811] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.815] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.817] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 06:06:11.820] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.821] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:06:11.824] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.824] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.826] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:06:11.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:06:11.949] [jointLog] [info] Computed 59,859 rich equivalence classes for further processing
[2020-02-07 06:06:11.949] [jointLog] [info] Counted 6,001,679 total reads in the equivalence classes 
[2020-02-07 06:06:11.963] [jointLog] [info] Number of mappings discarded because of alignment score : 580,291
[2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,871
[2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,293
[2020-02-07 06:06:11.963] [jointLog] [info] Mapping rate = 99.4934%

[2020-02-07 06:06:11.963] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 06:06:11.964] [jointLog] [info] Starting optimizer
[2020-02-07 06:06:11.980] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 06:06:11.983] [jointLog] [info] iteration = 0 | max rel diff. = 22288.5
[2020-02-07 06:06:11.949] [fileLog] [info] 
At end of round 0
==================
Observed 6032238 total fragments (6032238 in most recent round)

[2020-02-07 06:06:12.173] [jointLog] [info] iteration = 100 | max rel diff. = 5.81382
[2020-02-07 06:06:12.350] [jointLog] [info] iteration = 200 | max rel diff. = 1.42077
[2020-02-07 06:06:12.527] [jointLog] [info] iteration = 300 | max rel diff. = 1.66594
[2020-02-07 06:06:12.704] [jointLog] [info] iteration = 400 | max rel diff. = 0.0851054
[2020-02-07 06:06:12.881] [jointLog] [info] iteration = 500 | max rel diff. = 0.202441
[2020-02-07 06:06:13.058] [jointLog] [info] iteration = 600 | max rel diff. = 1.1212
[2020-02-07 06:06:13.235] [jointLog] [info] iteration = 700 | max rel diff. = 0.0507354
[2020-02-07 06:06:13.411] [jointLog] [info] iteration = 800 | max rel diff. = 0.132915
[2020-02-07 06:06:13.521] [jointLog] [info] iteration = 863 | max rel diff. = 0.00857531
[2020-02-07 06:06:13.522] [jointLog] [info] Finished optimizer
[2020-02-07 06:06:13.522] [jointLog] [info] writing output