[2020-04-26 00:18:34.720] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 00:18:34.720] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 00:18:34.720] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 00:18:34.720] [jointLog] [info] parsing read library format
[2020-04-26 00:18:34.720] [jointLog] [info] There is 1 library.
[2020-04-26 00:18:34.770] [jointLog] [info] Loading pufferfish index
[2020-04-26 00:18:34.770] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 00:18:34.845] [jointLog] [info] done
[2020-04-26 00:18:34.845] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 00:18:34.857] [jointLog] [info] Number of decoys : 0
[2020-04-26 00:18:46.268] [fileLog] [info] 
At end of round 0
==================
Observed 4311037 total fragments (4311037 in most recent round)

[2020-04-26 00:18:46.267] [jointLog] [info] Computed 99,603 rich equivalence classes for further processing
[2020-04-26 00:18:46.267] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes 
[2020-04-26 00:18:46.285] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,055
[2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025
[2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,876
[2020-04-26 00:18:46.289] [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 00:18:46.289] [jointLog] [info] Mapping rate = 99.2386%

[2020-04-26 00:18:46.289] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 00:18:46.290] [jointLog] [info] Starting optimizer
[2020-04-26 00:18:46.321] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 00:18:46.333] [jointLog] [info] iteration = 0 | max rel diff. = 9618.61
[2020-04-26 00:18:46.846] [jointLog] [info] iteration = 100 | max rel diff. = 6.9739
[2020-04-26 00:18:47.361] [jointLog] [info] iteration = 200 | max rel diff. = 4.22364
[2020-04-26 00:18:47.873] [jointLog] [info] iteration = 300 | max rel diff. = 0.295972
[2020-04-26 00:18:48.384] [jointLog] [info] iteration = 400 | max rel diff. = 0.455904
[2020-04-26 00:18:48.897] [jointLog] [info] iteration = 500 | max rel diff. = 0.130512
[2020-04-26 00:18:49.405] [jointLog] [info] iteration = 600 | max rel diff. = 5.60665
[2020-04-26 00:18:49.903] [jointLog] [info] iteration = 700 | max rel diff. = 0.0593442
[2020-04-26 00:18:50.410] [jointLog] [info] iteration = 800 | max rel diff. = 0.0590919
[2020-04-26 00:18:50.682] [jointLog] [info] iteration = 855 | max rel diff. = 0.00642465
[2020-04-26 00:18:50.684] [jointLog] [info] Finished optimizer
[2020-04-26 00:18:50.684] [jointLog] [info] writing output