[2020-04-26 09:51:22.976] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:51:22.976] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:51:22.976] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:51:22.976] [jointLog] [info] parsing read library format
[2020-04-26 09:51:22.976] [jointLog] [info] There is 1 library.
[2020-04-26 09:51:23.031] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:51:23.031] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:51:23.168] [jointLog] [info] done
[2020-04-26 09:51:23.168] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:51:23.181] [jointLog] [info] Number of decoys : 0
[2020-04-26 09:51:27.749] [jointLog] [info] Computed 53,884 rich equivalence classes for further processing
[2020-04-26 09:51:27.749] [jointLog] [info] Counted 1,453,009 total reads in the equivalence classes 
[2020-04-26 09:51:27.767] [jointLog] [info] Number of mappings discarded because of alignment score : 568,188
[2020-04-26 09:51:27.767] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,458
[2020-04-26 09:51:27.767] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 09:51:27.767] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,199
[2020-04-26 09:51:27.771] [jointLog] [warning] Only 1453009 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 09:51:27.771] [jointLog] [info] Mapping rate = 98.603%

[2020-04-26 09:51:27.771] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 09:51:27.772] [jointLog] [info] Starting optimizer
[2020-04-26 09:51:27.793] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 09:51:27.798] [jointLog] [info] iteration = 0 | max rel diff. = 3115.89
[2020-04-26 09:51:28.054] [jointLog] [info] iteration = 100 | max rel diff. = 16.0466
[2020-04-26 09:51:27.749] [fileLog] [info] 
At end of round 0
==================
Observed 1473595 total fragments (1473595 in most recent round)

[2020-04-26 09:51:28.304] [jointLog] [info] iteration = 200 | max rel diff. = 0.797743
[2020-04-26 09:51:28.555] [jointLog] [info] iteration = 300 | max rel diff. = 0.101302
[2020-04-26 09:51:28.805] [jointLog] [info] iteration = 400 | max rel diff. = 0.0485587
[2020-04-26 09:51:28.850] [jointLog] [info] iteration = 419 | max rel diff. = 0.00993705
[2020-04-26 09:51:28.851] [jointLog] [info] Finished optimizer
[2020-04-26 09:51:28.851] [jointLog] [info] writing output