[2020-04-26 05:35:22.725] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 05:35:22.725] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 05:35:22.725] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 05:35:22.725] [jointLog] [info] parsing read library format
[2020-04-26 05:35:22.725] [jointLog] [info] There is 1 library.
[2020-04-26 05:35:22.786] [jointLog] [info] Loading pufferfish index
[2020-04-26 05:35:22.786] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 05:35:22.965] [jointLog] [info] done
[2020-04-26 05:35:22.965] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 05:35:22.978] [jointLog] [info] Number of decoys : 0
[2020-04-26 05:35:23.729] [fileLog] [info] 
At end of round 0
==================
Observed 91614 total fragments (91614 in most recent round)

[2020-04-26 05:35:23.728] [jointLog] [info] Computed 21,384 rich equivalence classes for further processing
[2020-04-26 05:35:23.728] [jointLog] [info] Counted 79,375 total reads in the equivalence classes 
[2020-04-26 05:35:23.754] [jointLog] [info] Number of mappings discarded because of alignment score : 85,737
[2020-04-26 05:35:23.754] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,609
[2020-04-26 05:35:23.754] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 05:35:23.754] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 338
[2020-04-26 05:35:23.757] [jointLog] [warning] Only 79375 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 05:35:23.757] [jointLog] [info] Mapping rate = 86.6407%

[2020-04-26 05:35:23.757] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 05:35:23.759] [jointLog] [info] Starting optimizer
[2020-04-26 05:35:23.772] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 05:35:23.774] [jointLog] [info] iteration = 0 | max rel diff. = 190.226
[2020-04-26 05:35:23.890] [jointLog] [info] iteration = 100 | max rel diff. = 0.256567
[2020-04-26 05:35:23.974] [jointLog] [info] iteration = 176 | max rel diff. = 0.00479219
[2020-04-26 05:35:23.975] [jointLog] [info] Finished optimizer
[2020-04-26 05:35:23.975] [jointLog] [info] writing output