[2020-04-26 13:04:20.960] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 13:04:20.960] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 13:04:20.960] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 13:04:20.960] [jointLog] [info] parsing read library format
[2020-04-26 13:04:20.960] [jointLog] [info] There is 1 library.
[2020-04-26 13:04:21.026] [jointLog] [info] Loading pufferfish index
[2020-04-26 13:04:21.026] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 13:04:21.219] [jointLog] [info] done
[2020-04-26 13:04:21.219] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 13:04:21.233] [jointLog] [info] Number of decoys : 0
[2020-04-26 13:04:21.980] [fileLog] [info] 
At end of round 0
==================
Observed 78713 total fragments (78713 in most recent round)

[2020-04-26 13:04:21.980] [jointLog] [info] Computed 12,744 rich equivalence classes for further processing
[2020-04-26 13:04:21.980] [jointLog] [info] Counted 75,333 total reads in the equivalence classes 
[2020-04-26 13:04:22.012] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773
[2020-04-26 13:04:22.012] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953
[2020-04-26 13:04:22.012] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 13:04:22.012] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724
[2020-04-26 13:04:22.015] [jointLog] [warning] Only 75333 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 13:04:22.015] [jointLog] [info] Mapping rate = 95.7059%

[2020-04-26 13:04:22.015] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 13:04:22.016] [jointLog] [info] Starting optimizer
[2020-04-26 13:04:22.030] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 13:04:22.033] [jointLog] [info] iteration = 0 | max rel diff. = 146.196
[2020-04-26 13:04:22.129] [jointLog] [info] iteration = 100 | max rel diff. = 0.197249
[2020-04-26 13:04:22.183] [jointLog] [info] iteration = 161 | max rel diff. = 0.00158991
[2020-04-26 13:04:22.183] [jointLog] [info] Finished optimizer
[2020-04-26 13:04:22.183] [jointLog] [info] writing output