[2020-04-25 22:14:23.887] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 22:14:23.887] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 22:14:23.887] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 22:14:23.887] [jointLog] [info] parsing read library format
[2020-04-25 22:14:23.887] [jointLog] [info] There is 1 library.
[2020-04-25 22:14:23.941] [jointLog] [info] Loading pufferfish index
[2020-04-25 22:14:23.941] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 22:14:24.017] [jointLog] [info] done
[2020-04-25 22:14:24.017] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 22:14:24.028] [jointLog] [info] Number of decoys : 0
[2020-04-25 22:14:24.753] [fileLog] [info] 
At end of round 0
==================
Observed 91614 total fragments (91614 in most recent round)

[2020-04-25 22:14:24.753] [jointLog] [info] Computed 21,365 rich equivalence classes for further processing
[2020-04-25 22:14:24.753] [jointLog] [info] Counted 79,374 total reads in the equivalence classes 
[2020-04-25 22:14:24.772] [jointLog] [info] Number of mappings discarded because of alignment score : 85,738
[2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,610
[2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 338
[2020-04-25 22:14:24.775] [jointLog] [warning] Only 79374 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-25 22:14:24.775] [jointLog] [info] Mapping rate = 86.6396%

[2020-04-25 22:14:24.775] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 22:14:24.776] [jointLog] [info] Starting optimizer
[2020-04-25 22:14:24.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 22:14:24.793] [jointLog] [info] iteration = 0 | max rel diff. = 190.219
[2020-04-25 22:14:24.908] [jointLog] [info] iteration = 100 | max rel diff. = 0.229335
[2020-04-25 22:14:24.987] [jointLog] [info] iteration = 176 | max rel diff. = 0.00993408
[2020-04-25 22:14:24.987] [jointLog] [info] Finished optimizer
[2020-04-25 22:14:24.987] [jointLog] [info] writing output