[2020-04-25 21:31:19.311] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 21:31:19.311] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 21:31:19.311] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 21:31:19.311] [jointLog] [info] parsing read library format
[2020-04-25 21:31:19.311] [jointLog] [info] There is 1 library.
[2020-04-25 21:31:19.363] [jointLog] [info] Loading pufferfish index
[2020-04-25 21:31:19.363] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 21:31:19.438] [jointLog] [info] done
[2020-04-25 21:31:19.438] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 21:31:19.449] [jointLog] [info] Number of decoys : 0
[2020-04-25 21:31:25.760] [fileLog] [info] 
At end of round 0
==================
Observed 1973464 total fragments (1973464 in most recent round)

[2020-04-25 21:31:25.759] [jointLog] [info] Computed 65,127 rich equivalence classes for further processing
[2020-04-25 21:31:25.759] [jointLog] [info] Counted 1,951,686 total reads in the equivalence classes 
[2020-04-25 21:31:25.776] [jointLog] [info] Number of mappings discarded because of alignment score : 660,574
[2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,117
[2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,559
[2020-04-25 21:31:25.779] [jointLog] [warning] Only 1951686 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 21:31:25.779] [jointLog] [info] Mapping rate = 98.8965%

[2020-04-25 21:31:25.779] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 21:31:25.781] [jointLog] [info] Starting optimizer
[2020-04-25 21:31:25.801] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 21:31:25.809] [jointLog] [info] iteration = 0 | max rel diff. = 4061.37
[2020-04-25 21:31:26.233] [jointLog] [info] iteration = 100 | max rel diff. = 4.37046
[2020-04-25 21:31:26.657] [jointLog] [info] iteration = 200 | max rel diff. = 6.982
[2020-04-25 21:31:27.076] [jointLog] [info] iteration = 300 | max rel diff. = 0.26176
[2020-04-25 21:31:27.449] [jointLog] [info] iteration = 390 | max rel diff. = 0.00775314
[2020-04-25 21:31:27.449] [jointLog] [info] Finished optimizer
[2020-04-25 21:31:27.449] [jointLog] [info] writing output