[2020-04-25 23:52:36.960] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 23:52:36.960] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 23:52:36.960] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 23:52:36.960] [jointLog] [info] parsing read library format
[2020-04-25 23:52:36.960] [jointLog] [info] There is 1 library.
[2020-04-25 23:52:37.019] [jointLog] [info] Loading pufferfish index
[2020-04-25 23:52:37.019] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 23:52:37.261] [jointLog] [info] done
[2020-04-25 23:52:37.261] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 23:52:37.276] [jointLog] [info] Number of decoys : 0
[2020-04-25 23:52:43.368] [jointLog] [info] Computed 68,103 rich equivalence classes for further processing
[2020-04-25 23:52:43.368] [jointLog] [info] Counted 1,441,032 total reads in the equivalence classes 
[2020-04-25 23:52:43.390] [jointLog] [info] Number of mappings discarded because of alignment score : 600,985
[2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 15,865
[2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,603
[2020-04-25 23:52:43.395] [jointLog] [warning] Only 1441032 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 23:52:43.395] [jointLog] [info] Mapping rate = 98.8786%

[2020-04-25 23:52:43.395] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 23:52:43.396] [jointLog] [info] Starting optimizer
[2020-04-25 23:52:43.419] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 23:52:43.428] [jointLog] [info] iteration = 0 | max rel diff. = 3389.57
[2020-04-25 23:52:43.369] [fileLog] [info] 
At end of round 0
==================
Observed 1457375 total fragments (1457375 in most recent round)

[2020-04-25 23:52:43.804] [jointLog] [info] iteration = 100 | max rel diff. = 1.22199
[2020-04-25 23:52:44.190] [jointLog] [info] iteration = 200 | max rel diff. = 0.107501
[2020-04-25 23:52:44.576] [jointLog] [info] iteration = 300 | max rel diff. = 0.0774432
[2020-04-25 23:52:44.954] [jointLog] [info] iteration = 400 | max rel diff. = 0.043996
[2020-04-25 23:52:45.347] [jointLog] [info] iteration = 500 | max rel diff. = 0.0359073
[2020-04-25 23:52:45.731] [jointLog] [info] iteration = 599 | max rel diff. = 0.00158506
[2020-04-25 23:52:45.733] [jointLog] [info] Finished optimizer
[2020-04-25 23:52:45.733] [jointLog] [info] writing output