[2020-04-26 11:55:10.691] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 11:55:10.691] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 11:55:10.691] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 11:55:10.691] [jointLog] [info] parsing read library format
[2020-04-26 11:55:10.691] [jointLog] [info] There is 1 library.
[2020-04-26 11:55:10.756] [jointLog] [info] Loading pufferfish index
[2020-04-26 11:55:10.756] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 11:55:10.924] [jointLog] [info] done
[2020-04-26 11:55:10.924] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 11:55:10.939] [jointLog] [info] Number of decoys : 0
[2020-04-26 11:55:22.325] [fileLog] [info] 
At end of round 0
==================
Observed 4311037 total fragments (4311037 in most recent round)

[2020-04-26 11:55:22.324] [jointLog] [info] Computed 99,552 rich equivalence classes for further processing
[2020-04-26 11:55:22.324] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes 
[2020-04-26 11:55:22.344] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,048
[2020-04-26 11:55:22.344] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025
[2020-04-26 11:55:22.344] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 11:55:22.344] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,876
[2020-04-26 11:55:22.348] [jointLog] [warning] Only 4278214 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 11:55:22.348] [jointLog] [info] Mapping rate = 99.2386%

[2020-04-26 11:55:22.348] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 11:55:22.349] [jointLog] [info] Starting optimizer
[2020-04-26 11:55:22.373] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 11:55:22.383] [jointLog] [info] iteration = 0 | max rel diff. = 9616.98
[2020-04-26 11:55:22.909] [jointLog] [info] iteration = 100 | max rel diff. = 8.09992
[2020-04-26 11:55:23.430] [jointLog] [info] iteration = 200 | max rel diff. = 6.41828
[2020-04-26 11:55:23.954] [jointLog] [info] iteration = 300 | max rel diff. = 0.29969
[2020-04-26 11:55:24.474] [jointLog] [info] iteration = 400 | max rel diff. = 1.47263
[2020-04-26 11:55:24.991] [jointLog] [info] iteration = 500 | max rel diff. = 0.10742
[2020-04-26 11:55:25.501] [jointLog] [info] iteration = 600 | max rel diff. = 0.353468
[2020-04-26 11:55:26.015] [jointLog] [info] iteration = 700 | max rel diff. = 0.059426
[2020-04-26 11:55:26.509] [jointLog] [info] iteration = 800 | max rel diff. = 0.102779
[2020-04-26 11:55:26.847] [jointLog] [info] iteration = 870 | max rel diff. = 0.0034874
[2020-04-26 11:55:26.851] [jointLog] [info] Finished optimizer
[2020-04-26 11:55:26.851] [jointLog] [info] writing output