[2020-02-06 21:11:52.517] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 21:11:52.517] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 21:11:52.517] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 21:11:52.517] [jointLog] [info] parsing read library format
[2020-02-06 21:11:52.517] [jointLog] [info] There is 1 library.
[2020-02-06 21:11:52.588] [jointLog] [info] Loading pufferfish index
[2020-02-06 21:11:52.588] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 21:11:53.799] [jointLog] [info] done
[2020-02-06 21:11:53.799] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 21:11:53.815] [jointLog] [info] Number of decoys : 0
[2020-02-06 21:12:09.990] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:09.994] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:12:10.003] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.008] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.011] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:12:10.013] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.020] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.037] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.042] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.047] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.049] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.055] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.072] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-06 21:12:10.096] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-06 21:12:10.104] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.107] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.109] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.109] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.112] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.115] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.115] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 21:12:10.116] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 21:12:10.117] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:12:10.117] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.119] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.120] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 21:12:10.120] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 21:12:10.123] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments
[2020-02-06 21:12:10.269] [jointLog] [info] Computed 46,334 rich equivalence classes for further processing
[2020-02-06 21:12:10.269] [jointLog] [info] Counted 6,295,903 total reads in the equivalence classes 
[2020-02-06 21:12:10.284] [jointLog] [info] Number of mappings discarded because of alignment score : 724,619
[2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,735
[2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,420
[2020-02-06 21:12:10.284] [jointLog] [info] Mapping rate = 99.5522%

[2020-02-06 21:12:10.284] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 21:12:10.285] [jointLog] [info] Starting optimizer
[2020-02-06 21:12:10.301] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 21:12:10.304] [jointLog] [info] iteration = 0 | max rel diff. = 26951.6
[2020-02-06 21:12:10.494] [jointLog] [info] iteration = 100 | max rel diff. = 5.50074
[2020-02-06 21:12:10.651] [jointLog] [info] iteration = 200 | max rel diff. = 2.0893
[2020-02-06 21:12:10.270] [fileLog] [info] 
At end of round 0
==================
Observed 6324223 total fragments (6324223 in most recent round)

[2020-02-06 21:12:10.808] [jointLog] [info] iteration = 300 | max rel diff. = 0.164198
[2020-02-06 21:12:10.966] [jointLog] [info] iteration = 400 | max rel diff. = 0.0470168
[2020-02-06 21:12:11.124] [jointLog] [info] iteration = 500 | max rel diff. = 0.0494535
[2020-02-06 21:12:11.281] [jointLog] [info] iteration = 600 | max rel diff. = 0.0402461
[2020-02-06 21:12:11.395] [jointLog] [info] iteration = 674 | max rel diff. = 0.00996907
[2020-02-06 21:12:11.396] [jointLog] [info] Finished optimizer
[2020-02-06 21:12:11.396] [jointLog] [info] writing output