[2020-04-25 22:48:41.221] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 22:48:41.221] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 22:48:41.221] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 22:48:41.221] [jointLog] [info] parsing read library format
[2020-04-25 22:48:41.221] [jointLog] [info] There is 1 library.
[2020-04-25 22:48:41.278] [jointLog] [info] Loading pufferfish index
[2020-04-25 22:48:41.278] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 22:48:41.359] [jointLog] [info] done
[2020-04-25 22:48:41.359] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 22:48:41.373] [jointLog] [info] Number of decoys : 0
[2020-04-25 22:48:49.132] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-25 22:48:49.131] [jointLog] [info] Computed 81,404 rich equivalence classes for further processing
[2020-04-25 22:48:49.131] [jointLog] [info] Counted 2,537,570 total reads in the equivalence classes 
[2020-04-25 22:48:49.153] [jointLog] [info] Number of mappings discarded because of alignment score : 763,754
[2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,278
[2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111
[2020-04-25 22:48:49.157] [jointLog] [warning] Only 2537570 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 22:48:49.157] [jointLog] [info] Mapping rate = 98.9786%

[2020-04-25 22:48:49.157] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 22:48:49.158] [jointLog] [info] Starting optimizer
[2020-04-25 22:48:49.187] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 22:48:49.194] [jointLog] [info] iteration = 0 | max rel diff. = 5795.65
[2020-04-25 22:48:49.529] [jointLog] [info] iteration = 100 | max rel diff. = 8.26659
[2020-04-25 22:48:49.861] [jointLog] [info] iteration = 200 | max rel diff. = 13.2913
[2020-04-25 22:48:50.191] [jointLog] [info] iteration = 300 | max rel diff. = 0.671813
[2020-04-25 22:48:50.520] [jointLog] [info] iteration = 400 | max rel diff. = 0.0579421
[2020-04-25 22:48:50.841] [jointLog] [info] iteration = 500 | max rel diff. = 0.275643
[2020-04-25 22:48:51.166] [jointLog] [info] iteration = 600 | max rel diff. = 0.395018
[2020-04-25 22:48:51.478] [jointLog] [info] iteration = 696 | max rel diff. = 0.0086757
[2020-04-25 22:48:51.482] [jointLog] [info] Finished optimizer
[2020-04-25 22:48:51.482] [jointLog] [info] writing output