[2020-04-25 20:39:19.031] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 20:39:19.031] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 20:39:19.031] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 20:39:19.031] [jointLog] [info] parsing read library format
[2020-04-25 20:39:19.031] [jointLog] [info] There is 1 library.
[2020-04-25 20:39:19.090] [jointLog] [info] Loading pufferfish index
[2020-04-25 20:39:19.090] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 20:39:19.173] [jointLog] [info] done
[2020-04-25 20:39:19.173] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 20:39:19.186] [jointLog] [info] Number of decoys : 0
[2020-04-25 20:39:24.890] [jointLog] [info] Computed 81,782 rich equivalence classes for further processing
[2020-04-25 20:39:24.890] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes 
[2020-04-25 20:39:24.916] [jointLog] [info] Number of mappings discarded because of alignment score : 733,448
[2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154
[2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582
[2020-04-25 20:39:24.920] [jointLog] [warning] Only 1745454 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 20:39:24.920] [jointLog] [info] Mapping rate = 98.6937%

[2020-04-25 20:39:24.920] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 20:39:24.922] [jointLog] [info] Starting optimizer
[2020-04-25 20:39:24.950] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 20:39:24.957] [jointLog] [info] iteration = 0 | max rel diff. = 3746.91
[2020-04-25 20:39:24.891] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-25 20:39:25.319] [jointLog] [info] iteration = 100 | max rel diff. = 3.67314
[2020-04-25 20:39:25.676] [jointLog] [info] iteration = 200 | max rel diff. = 13.2264
[2020-04-25 20:39:26.036] [jointLog] [info] iteration = 300 | max rel diff. = 0.656034
[2020-04-25 20:39:26.293] [jointLog] [info] iteration = 374 | max rel diff. = 0.00980363
[2020-04-25 20:39:26.294] [jointLog] [info] Finished optimizer
[2020-04-25 20:39:26.294] [jointLog] [info] writing output