[2020-04-26 03:40:24.289] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 03:40:24.289] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 03:40:24.289] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 03:40:24.289] [jointLog] [info] parsing read library format
[2020-04-26 03:40:24.289] [jointLog] [info] There is 1 library.
[2020-04-26 03:40:24.351] [jointLog] [info] Loading pufferfish index
[2020-04-26 03:40:24.351] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 03:40:24.488] [jointLog] [info] done
[2020-04-26 03:40:24.488] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 03:40:24.502] [jointLog] [info] Number of decoys : 0
[2020-04-26 03:40:31.641] [jointLog] [info] Computed 81,264 rich equivalence classes for further processing
[2020-04-26 03:40:31.641] [jointLog] [info] Counted 2,537,571 total reads in the equivalence classes 
[2020-04-26 03:40:31.661] [jointLog] [info] Number of mappings discarded because of alignment score : 763,753
[2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,277
[2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111
[2020-04-26 03:40:31.665] [jointLog] [warning] Only 2537571 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 03:40:31.665] [jointLog] [info] Mapping rate = 98.9787%

[2020-04-26 03:40:31.665] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 03:40:31.667] [jointLog] [info] Starting optimizer
[2020-04-26 03:40:31.690] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 03:40:31.695] [jointLog] [info] iteration = 0 | max rel diff. = 5796.83
[2020-04-26 03:40:31.642] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-26 03:40:32.015] [jointLog] [info] iteration = 100 | max rel diff. = 8.1899
[2020-04-26 03:40:32.329] [jointLog] [info] iteration = 200 | max rel diff. = 3.8306
[2020-04-26 03:40:32.652] [jointLog] [info] iteration = 300 | max rel diff. = 7.41525
[2020-04-26 03:40:32.975] [jointLog] [info] iteration = 400 | max rel diff. = 3.06393
[2020-04-26 03:40:33.295] [jointLog] [info] iteration = 500 | max rel diff. = 0.139388
[2020-04-26 03:40:33.615] [jointLog] [info] iteration = 600 | max rel diff. = 0.0488443
[2020-04-26 03:40:33.941] [jointLog] [info] iteration = 700 | max rel diff. = 0.0278767
[2020-04-26 03:40:34.242] [jointLog] [info] iteration = 797 | max rel diff. = 0.00852398
[2020-04-26 03:40:34.243] [jointLog] [info] Finished optimizer
[2020-04-26 03:40:34.243] [jointLog] [info] writing output