[2020-04-26 12:38:31.394] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 12:38:31.394] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 12:38:31.394] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 12:38:31.394] [jointLog] [info] parsing read library format
[2020-04-26 12:38:31.394] [jointLog] [info] There is 1 library.
[2020-04-26 12:38:31.461] [jointLog] [info] Loading pufferfish index
[2020-04-26 12:38:31.461] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 12:38:31.622] [jointLog] [info] done
[2020-04-26 12:38:31.622] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 12:38:31.635] [jointLog] [info] Number of decoys : 0
[2020-04-26 12:38:33.518] [fileLog] [info] 
At end of round 0
==================
Observed 402112 total fragments (402112 in most recent round)

[2020-04-26 12:38:33.518] [jointLog] [info] Computed 34,344 rich equivalence classes for further processing
[2020-04-26 12:38:33.518] [jointLog] [info] Counted 379,958 total reads in the equivalence classes 
[2020-04-26 12:38:33.556] [jointLog] [info] Number of mappings discarded because of alignment score : 250,107
[2020-04-26 12:38:33.556] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,667
[2020-04-26 12:38:33.556] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 12:38:33.556] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 899
[2020-04-26 12:38:33.560] [jointLog] [warning] Only 379958 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 12:38:33.560] [jointLog] [info] Mapping rate = 94.4906%

[2020-04-26 12:38:33.560] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 12:38:33.562] [jointLog] [info] Starting optimizer
[2020-04-26 12:38:33.580] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 12:38:33.584] [jointLog] [info] iteration = 0 | max rel diff. = 902.487
[2020-04-26 12:38:33.781] [jointLog] [info] iteration = 100 | max rel diff. = 20.3944
[2020-04-26 12:38:33.973] [jointLog] [info] iteration = 200 | max rel diff. = 0.0661397
[2020-04-26 12:38:34.168] [jointLog] [info] iteration = 300 | max rel diff. = 0.853932
[2020-04-26 12:38:34.359] [jointLog] [info] iteration = 400 | max rel diff. = 0.572984
[2020-04-26 12:38:34.550] [jointLog] [info] iteration = 500 | max rel diff. = 0.244242
[2020-04-26 12:38:34.578] [jointLog] [info] iteration = 515 | max rel diff. = 0.000646853
[2020-04-26 12:38:34.579] [jointLog] [info] Finished optimizer
[2020-04-26 12:38:34.579] [jointLog] [info] writing output