[2020-04-25 23:31:47.192] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 23:31:47.192] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 23:31:47.192] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 23:31:47.192] [jointLog] [info] parsing read library format
[2020-04-25 23:31:47.192] [jointLog] [info] There is 1 library.
[2020-04-25 23:31:47.249] [jointLog] [info] Loading pufferfish index
[2020-04-25 23:31:47.249] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 23:31:47.397] [jointLog] [info] done
[2020-04-25 23:31:47.397] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 23:31:47.411] [jointLog] [info] Number of decoys : 0
[2020-04-25 23:31:48.638] [fileLog] [info] 
At end of round 0
==================
Observed 101774 total fragments (101774 in most recent round)

[2020-04-25 23:31:48.638] [jointLog] [info] Computed 8,701 rich equivalence classes for further processing
[2020-04-25 23:31:48.638] [jointLog] [info] Counted 91,344 total reads in the equivalence classes 
[2020-04-25 23:31:48.663] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787
[2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280
[2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518
[2020-04-25 23:31:48.666] [jointLog] [warning] Only 91344 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 23:31:48.666] [jointLog] [info] Mapping rate = 89.7518%

[2020-04-25 23:31:48.666] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 23:31:48.668] [jointLog] [info] Starting optimizer
[2020-04-25 23:31:48.683] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 23:31:48.685] [jointLog] [info] iteration = 0 | max rel diff. = 223.403
[2020-04-25 23:31:48.780] [jointLog] [info] iteration = 100 | max rel diff. = 0.164675
[2020-04-25 23:31:48.867] [jointLog] [info] iteration = 200 | max rel diff. = 0.0355829
[2020-04-25 23:31:48.910] [jointLog] [info] iteration = 253 | max rel diff. = 0.00668343
[2020-04-25 23:31:48.911] [jointLog] [info] Finished optimizer
[2020-04-25 23:31:48.911] [jointLog] [info] writing output