[2020-04-06 17:23:20.517] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-06 17:23:20.517] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-06 17:23:20.517] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-06 17:23:20.517] [jointLog] [info] parsing read library format
[2020-04-06 17:23:20.517] [jointLog] [info] There is 1 library.
[2020-04-06 17:23:20.583] [jointLog] [info] Loading pufferfish index
[2020-04-06 17:23:20.583] [jointLog] [info] Loading dense pufferfish index.
[2020-04-06 17:23:20.601] [jointLog] [info] done
[2020-04-06 17:23:20.601] [jointLog] [info] Index contained 5,183 targets
[2020-04-06 17:23:20.604] [jointLog] [info] Number of decoys : 0
[2020-04-06 17:23:22.734] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.763] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.772] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.783] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.800] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.819] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:23:22.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.837] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.844] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.858] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.873] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.881] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.883] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.903] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-04-06 17:23:22.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.907] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:23:22.914] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:23:22.923] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:23:22.925] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:23:23.124] [jointLog] [info] Computed 9,691 rich equivalence classes for further processing
[2020-04-06 17:23:23.124] [jointLog] [info] Counted 707,579 total reads in the equivalence classes 
[2020-04-06 17:23:23.137] [jointLog] [info] Number of mappings discarded because of alignment score : 26,250
[2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,962
[2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 57
[2020-04-06 17:23:23.137] [jointLog] [warning] Only 707579 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-06 17:23:23.137] [jointLog] [info] Mapping rate = 98.8607%

[2020-04-06 17:23:23.137] [jointLog] [info] finished quantifyLibrary()
[2020-04-06 17:23:23.138] [jointLog] [info] Starting optimizer
[2020-04-06 17:23:23.144] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-06 17:23:23.145] [jointLog] [info] iteration = 0 | max rel diff. = 7173.08
[2020-04-06 17:23:23.179] [jointLog] [info] iteration = 100 | max rel diff. = 0.337263
[2020-04-06 17:23:23.124] [fileLog] [info] 
At end of round 0
==================
Observed 715733 total fragments (715733 in most recent round)

[2020-04-06 17:23:23.210] [jointLog] [info] iteration = 200 | max rel diff. = 0.0168808
[2020-04-06 17:23:23.240] [jointLog] [info] iteration = 300 | max rel diff. = 0.0832982
[2020-04-06 17:23:23.255] [jointLog] [info] iteration = 357 | max rel diff. = 0.00142306
[2020-04-06 17:23:23.255] [jointLog] [info] Finished optimizer
[2020-04-06 17:23:23.255] [jointLog] [info] writing output