[2020-02-07 11:13:18.756] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-07 11:13:18.756] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-07 11:13:18.756] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-07 11:13:18.756] [jointLog] [info] parsing read library format
[2020-02-07 11:13:18.756] [jointLog] [info] There is 1 library.
[2020-02-07 11:13:18.834] [jointLog] [info] Loading pufferfish index
[2020-02-07 11:13:18.835] [jointLog] [info] Loading dense pufferfish index.
[2020-02-07 11:13:18.927] [jointLog] [info] done
[2020-02-07 11:13:18.927] [jointLog] [info] Index contained 19,670 targets
[2020-02-07 11:13:18.937] [jointLog] [info] Number of decoys : 0
[2020-02-07 11:13:36.866] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.872] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 11:13:36.873] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 11:13:36.886] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.886] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.891] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.894] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.895] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.899] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.903] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.905] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.909] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.913] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments
[2020-02-07 11:13:36.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.945] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.947] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-07 11:13:36.949] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.951] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.954] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.955] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 11:13:36.956] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-07 11:13:36.963] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 11:13:36.964] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.966] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-07 11:13:36.967] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:36.968] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-07 11:13:36.970] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-07 11:13:37.116] [jointLog] [info] Computed 59,752 rich equivalence classes for further processing
[2020-02-07 11:13:37.116] [jointLog] [info] Counted 6,001,688 total reads in the equivalence classes 
[2020-02-07 11:13:37.131] [jointLog] [info] Number of mappings discarded because of alignment score : 580,149
[2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,872
[2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,290
[2020-02-07 11:13:37.131] [jointLog] [info] Mapping rate = 99.4936%

[2020-02-07 11:13:37.131] [jointLog] [info] finished quantifyLibrary()
[2020-02-07 11:13:37.132] [jointLog] [info] Starting optimizer
[2020-02-07 11:13:37.152] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-07 11:13:37.154] [jointLog] [info] iteration = 0 | max rel diff. = 22279.9
[2020-02-07 11:13:37.342] [jointLog] [info] iteration = 100 | max rel diff. = 4.47678
[2020-02-07 11:13:37.117] [fileLog] [info] 
At end of round 0
==================
Observed 6032238 total fragments (6032238 in most recent round)

[2020-02-07 11:13:37.507] [jointLog] [info] iteration = 200 | max rel diff. = 1.33114
[2020-02-07 11:13:37.671] [jointLog] [info] iteration = 300 | max rel diff. = 1.96155
[2020-02-07 11:13:37.835] [jointLog] [info] iteration = 400 | max rel diff. = 0.062511
[2020-02-07 11:13:38.000] [jointLog] [info] iteration = 500 | max rel diff. = 0.238749
[2020-02-07 11:13:38.164] [jointLog] [info] iteration = 600 | max rel diff. = 0.0848667
[2020-02-07 11:13:38.328] [jointLog] [info] iteration = 700 | max rel diff. = 0.0242495
[2020-02-07 11:13:38.493] [jointLog] [info] iteration = 800 | max rel diff. = 0.104385
[2020-02-07 11:13:38.657] [jointLog] [info] iteration = 900 | max rel diff. = 0.0214139
[2020-02-07 11:13:38.731] [jointLog] [info] iteration = 946 | max rel diff. = 0.00394748
[2020-02-07 11:13:38.732] [jointLog] [info] Finished optimizer
[2020-02-07 11:13:38.732] [jointLog] [info] writing output