[2020-04-25 20:30:39.229] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 20:30:39.229] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 20:30:39.229] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 20:30:39.229] [jointLog] [info] parsing read library format
[2020-04-25 20:30:39.229] [jointLog] [info] There is 1 library.
[2020-04-25 20:30:39.294] [jointLog] [info] Loading pufferfish index
[2020-04-25 20:30:39.294] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 20:30:39.633] [jointLog] [info] done
[2020-04-25 20:30:39.633] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 20:30:39.655] [jointLog] [info] Number of decoys : 0
[2020-04-25 20:30:45.874] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-25 20:30:45.874] [jointLog] [info] Computed 76,452 rich equivalence classes for further processing
[2020-04-25 20:30:45.874] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes 
[2020-04-25 20:30:45.893] [jointLog] [info] Number of mappings discarded because of alignment score : 536,820
[2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061
[2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328
[2020-04-25 20:30:45.897] [jointLog] [warning] Only 2319185 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 20:30:45.897] [jointLog] [info] Mapping rate = 99.1791%

[2020-04-25 20:30:45.897] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 20:30:45.899] [jointLog] [info] Starting optimizer
[2020-04-25 20:30:45.920] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 20:30:45.925] [jointLog] [info] iteration = 0 | max rel diff. = 4684.76
[2020-04-25 20:30:46.219] [jointLog] [info] iteration = 100 | max rel diff. = 3.31511
[2020-04-25 20:30:46.502] [jointLog] [info] iteration = 200 | max rel diff. = 1.94852
[2020-04-25 20:30:46.789] [jointLog] [info] iteration = 300 | max rel diff. = 0.490505
[2020-04-25 20:30:47.075] [jointLog] [info] iteration = 400 | max rel diff. = 0.0589214
[2020-04-25 20:30:47.362] [jointLog] [info] iteration = 500 | max rel diff. = 0.302249
[2020-04-25 20:30:47.654] [jointLog] [info] iteration = 600 | max rel diff. = 0.155543
[2020-04-25 20:30:47.946] [jointLog] [info] iteration = 700 | max rel diff. = 0.059642
[2020-04-25 20:30:48.232] [jointLog] [info] iteration = 800 | max rel diff. = 0.13392
[2020-04-25 20:30:48.522] [jointLog] [info] iteration = 900 | max rel diff. = 0.00822358
[2020-04-25 20:30:48.526] [jointLog] [info] Finished optimizer
[2020-04-25 20:30:48.526] [jointLog] [info] writing output