[2020-02-06 18:40:08.848] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 18:40:08.848] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 18:40:08.848] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 18:40:08.848] [jointLog] [info] parsing read library format
[2020-02-06 18:40:08.848] [jointLog] [info] There is 1 library.
[2020-02-06 18:40:08.914] [jointLog] [info] Loading pufferfish index
[2020-02-06 18:40:08.914] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 18:40:10.048] [jointLog] [info] done
[2020-02-06 18:40:10.048] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 18:40:10.064] [jointLog] [info] Number of decoys : 0
[2020-02-06 18:40:25.991] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:25.992] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:40:25.993] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.006] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.008] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.009] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.016] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.019] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:40:26.025] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.026] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.031] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.034] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.037] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.037] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments
[2020-02-06 18:40:26.057] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.060] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.071] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.072] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.076] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.083] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:40:26.084] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.086] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:40:26.092] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.092] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.097] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.097] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:40:26.098] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2020-02-06 18:40:26.102] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:40:26.286] [jointLog] [info] Computed 59,767 rich equivalence classes for further processing
[2020-02-06 18:40:26.286] [jointLog] [info] Counted 6,001,661 total reads in the equivalence classes 
[2020-02-06 18:40:26.299] [jointLog] [info] Number of mappings discarded because of alignment score : 580,179
[2020-02-06 18:40:26.299] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,889
[2020-02-06 18:40:26.299] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 18:40:26.299] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,294
[2020-02-06 18:40:26.299] [jointLog] [info] Mapping rate = 99.4931%

[2020-02-06 18:40:26.299] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 18:40:26.300] [jointLog] [info] Starting optimizer
[2020-02-06 18:40:26.315] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 18:40:26.318] [jointLog] [info] iteration = 0 | max rel diff. = 22279.1
[2020-02-06 18:40:26.528] [jointLog] [info] iteration = 100 | max rel diff. = 17.6322
[2020-02-06 18:40:26.286] [fileLog] [info] 
At end of round 0
==================
Observed 6032238 total fragments (6032238 in most recent round)

[2020-02-06 18:40:26.702] [jointLog] [info] iteration = 200 | max rel diff. = 1.69564
[2020-02-06 18:40:26.885] [jointLog] [info] iteration = 300 | max rel diff. = 2.7112
[2020-02-06 18:40:27.060] [jointLog] [info] iteration = 400 | max rel diff. = 0.259789
[2020-02-06 18:40:27.234] [jointLog] [info] iteration = 500 | max rel diff. = 0.164122
[2020-02-06 18:40:27.408] [jointLog] [info] iteration = 600 | max rel diff. = 0.427842
[2020-02-06 18:40:27.583] [jointLog] [info] iteration = 700 | max rel diff. = 0.0252609
[2020-02-06 18:40:27.757] [jointLog] [info] iteration = 800 | max rel diff. = 0.13804
[2020-02-06 18:40:27.860] [jointLog] [info] iteration = 860 | max rel diff. = 0.00894765
[2020-02-06 18:40:27.860] [jointLog] [info] Finished optimizer
[2020-02-06 18:40:27.860] [jointLog] [info] writing output