[2020-02-07 06:29:45.123] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 06:29:45.123] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 06:29:45.123] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 06:29:45.123] [jointLog] [info] parsing read library format
[2020-02-07 06:29:45.124] [jointLog] [info] There is 1 library.
[2020-02-07 06:29:45.203] [jointLog] [info] Loading pufferfish index
[2020-02-07 06:29:45.203] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 06:29:45.312] [jointLog] [info] done
[2020-02-07 06:29:45.312] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 06:29:45.322] [jointLog] [info] Number of decoys : 0
[2020-02-07 06:30:03.687] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.688] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.693] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:30:03.698] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.707] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.709] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:30:03.714] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.725] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.727] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.730] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments
[2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-07 06:30:03.768] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.769] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 06:30:03.775] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.777] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.778] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:30:03.782] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.785] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 06:30:03.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 06:30:03.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.796] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 06:30:03.798] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-07 06:30:03.923] [jointLog] [info] Computed 46,457 rich equivalence classes for further processing
[2020-02-07 06:30:03.923] [jointLog] [info] Counted 6,295,944 total reads in the equivalence classes 
[2020-02-07 06:30:03.938] [jointLog] [info] Number of mappings discarded because of alignment score : 725,182
[2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,693
[2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,422
[2020-02-07 06:30:03.938] [jointLog] [info] Mapping rate = 99.5528%

[2020-02-07 06:30:03.938] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 06:30:03.940] [jointLog] [info] Starting optimizer
[2020-02-07 06:30:03.953] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 06:30:03.955] [jointLog] [info] iteration = 0 | max rel diff. = 26946.6
[2020-02-07 06:30:04.112] [jointLog] [info] iteration = 100 | max rel diff. = 4.98452
[2020-02-07 06:30:04.262] [jointLog] [info] iteration = 200 | max rel diff. = 2.93961
[2020-02-07 06:30:03.923] [fileLog] [info] 
At end of round 0
==================
Observed 6324223 total fragments (6324223 in most recent round)

[2020-02-07 06:30:04.412] [jointLog] [info] iteration = 300 | max rel diff. = 0.165184
[2020-02-07 06:30:04.562] [jointLog] [info] iteration = 400 | max rel diff. = 0.17632
[2020-02-07 06:30:04.712] [jointLog] [info] iteration = 500 | max rel diff. = 0.0485105
[2020-02-07 06:30:04.862] [jointLog] [info] iteration = 600 | max rel diff. = 0.0677893
[2020-02-07 06:30:04.977] [jointLog] [info] iteration = 677 | max rel diff. = 0.0098568
[2020-02-07 06:30:04.978] [jointLog] [info] Finished optimizer
[2020-02-07 06:30:04.978] [jointLog] [info] writing output