[2020-04-26 00:01:16.256] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 00:01:16.256] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 00:01:16.256] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 00:01:16.256] [jointLog] [info] parsing read library format
[2020-04-26 00:01:16.256] [jointLog] [info] There is 1 library.
[2020-04-26 00:01:16.314] [jointLog] [info] Loading pufferfish index
[2020-04-26 00:01:16.314] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 00:01:16.509] [jointLog] [info] done
[2020-04-26 00:01:16.509] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 00:01:16.522] [jointLog] [info] Number of decoys : 0
[2020-04-26 00:01:22.869] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-26 00:01:22.869] [jointLog] [info] Computed 76,483 rich equivalence classes for further processing
[2020-04-26 00:01:22.869] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes 
[2020-04-26 00:01:22.887] [jointLog] [info] Number of mappings discarded because of alignment score : 536,826
[2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061
[2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328
[2020-04-26 00:01:22.890] [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.

[2020-04-26 00:01:22.890] [jointLog] [info] Mapping rate = 99.1791%

[2020-04-26 00:01:22.890] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 00:01:22.892] [jointLog] [info] Starting optimizer
[2020-04-26 00:01:22.916] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 00:01:22.922] [jointLog] [info] iteration = 0 | max rel diff. = 4684.51
[2020-04-26 00:01:23.217] [jointLog] [info] iteration = 100 | max rel diff. = 4.41794
[2020-04-26 00:01:23.508] [jointLog] [info] iteration = 200 | max rel diff. = 2.96994
[2020-04-26 00:01:23.799] [jointLog] [info] iteration = 300 | max rel diff. = 0.713546
[2020-04-26 00:01:24.093] [jointLog] [info] iteration = 400 | max rel diff. = 0.224459
[2020-04-26 00:01:24.392] [jointLog] [info] iteration = 500 | max rel diff. = 0.106728
[2020-04-26 00:01:24.685] [jointLog] [info] iteration = 600 | max rel diff. = 1.1458
[2020-04-26 00:01:24.972] [jointLog] [info] iteration = 700 | max rel diff. = 0.0266081
[2020-04-26 00:01:25.250] [jointLog] [info] iteration = 800 | max rel diff. = 0.0567766
[2020-04-26 00:01:25.512] [jointLog] [info] iteration = 894 | max rel diff. = 0.00747066
[2020-04-26 00:01:25.513] [jointLog] [info] Finished optimizer
[2020-04-26 00:01:25.513] [jointLog] [info] writing output