[2020-02-07 08:36:35.360] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 08:36:35.360] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 08:36:35.360] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 08:36:35.360] [jointLog] [info] parsing read library format
[2020-02-07 08:36:35.360] [jointLog] [info] There is 1 library.
[2020-02-07 08:36:35.419] [jointLog] [info] Loading pufferfish index
[2020-02-07 08:36:35.419] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 08:36:35.612] [jointLog] [info] done
[2020-02-07 08:36:35.612] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 08:36:35.621] [jointLog] [info] Number of decoys : 0
[2020-02-07 08:36:51.624] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.627] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.634] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:36:51.642] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.643] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:36:51.650] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.650] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:36:51.653] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.655] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.657] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.659] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.662] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.685] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.698] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.702] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.704] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 08:36:51.707] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.709] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.712] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:36:51.724] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:36:51.726] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.732] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 08:36:51.733] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:36:51.733] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.734] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.736] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 08:36:51.737] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 08:36:51.741] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 08:36:51.869] [jointLog] [info] Computed 56,008 rich equivalence classes for further processing
[2020-02-07 08:36:51.869] [jointLog] [info] Counted 6,861,107 total reads in the equivalence classes 
[2020-02-07 08:36:51.885] [jointLog] [info] Number of mappings discarded because of alignment score : 915,582
[2020-02-07 08:36:51.885] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,651
[2020-02-07 08:36:51.885] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 08:36:51.885] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,059
[2020-02-07 08:36:51.885] [jointLog] [info] Mapping rate = 99.5862%

[2020-02-07 08:36:51.885] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 08:36:51.886] [jointLog] [info] Starting optimizer
[2020-02-07 08:36:51.907] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 08:36:51.911] [jointLog] [info] iteration = 0 | max rel diff. = 29789.5
[2020-02-07 08:36:51.869] [fileLog] [info] 
At end of round 0
==================
Observed 6889615 total fragments (6889615 in most recent round)

[2020-02-07 08:36:52.172] [jointLog] [info] iteration = 100 | max rel diff. = 3.05436
[2020-02-07 08:36:52.399] [jointLog] [info] iteration = 200 | max rel diff. = 0.397386
[2020-02-07 08:36:52.627] [jointLog] [info] iteration = 300 | max rel diff. = 2.64687
[2020-02-07 08:36:52.856] [jointLog] [info] iteration = 400 | max rel diff. = 5.2758
[2020-02-07 08:36:53.089] [jointLog] [info] iteration = 500 | max rel diff. = 0.350971
[2020-02-07 08:36:53.316] [jointLog] [info] iteration = 600 | max rel diff. = 0.240883
[2020-02-07 08:36:53.544] [jointLog] [info] iteration = 700 | max rel diff. = 0.0416519
[2020-02-07 08:36:53.608] [jointLog] [info] iteration = 729 | max rel diff. = 0.00433551
[2020-02-07 08:36:53.609] [jointLog] [info] Finished optimizer
[2020-02-07 08:36:53.609] [jointLog] [info] writing output