[2020-04-25 22:40:09.966] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 22:40:09.966] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 22:40:09.966] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 22:40:09.966] [jointLog] [info] parsing read library format
[2020-04-25 22:40:09.966] [jointLog] [info] There is 1 library.
[2020-04-25 22:40:10.022] [jointLog] [info] Loading pufferfish index
[2020-04-25 22:40:10.022] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 22:40:10.104] [jointLog] [info] done
[2020-04-25 22:40:10.104] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 22:40:10.117] [jointLog] [info] Number of decoys : 0
[2020-04-25 22:40:11.012] [fileLog] [info] 
At end of round 0
==================
Observed 56697 total fragments (56697 in most recent round)

[2020-04-25 22:40:11.011] [jointLog] [info] Computed 8,592 rich equivalence classes for further processing
[2020-04-25 22:40:11.011] [jointLog] [info] Counted 49,503 total reads in the equivalence classes 
[2020-04-25 22:40:11.046] [jointLog] [info] Number of mappings discarded because of alignment score : 49,151
[2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,787
[2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 268
[2020-04-25 22:40:11.049] [jointLog] [warning] Only 49503 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-25 22:40:11.049] [jointLog] [info] Mapping rate = 87.3115%

[2020-04-25 22:40:11.049] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 22:40:11.050] [jointLog] [info] Starting optimizer
[2020-04-25 22:40:11.065] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 22:40:11.067] [jointLog] [info] iteration = 0 | max rel diff. = 119.435
[2020-04-25 22:40:11.141] [jointLog] [info] iteration = 100 | max rel diff. = 0.883259
[2020-04-25 22:40:11.209] [jointLog] [info] iteration = 200 | max rel diff. = 0.276108
[2020-04-25 22:40:11.216] [jointLog] [info] iteration = 212 | max rel diff. = 0.00763359
[2020-04-25 22:40:11.217] [jointLog] [info] Finished optimizer
[2020-04-25 22:40:11.217] [jointLog] [info] writing output