[2020-04-25 21:05:19.755] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 21:05:19.755] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 21:05:19.755] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 21:05:19.755] [jointLog] [info] parsing read library format
[2020-04-25 21:05:19.755] [jointLog] [info] There is 1 library.
[2020-04-25 21:05:19.807] [jointLog] [info] Loading pufferfish index
[2020-04-25 21:05:19.807] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 21:05:20.030] [jointLog] [info] done
[2020-04-25 21:05:20.030] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 21:05:20.044] [jointLog] [info] Number of decoys : 0
[2020-04-25 21:05:30.070] [jointLog] [info] Computed 93,649 rich equivalence classes for further processing
[2020-04-25 21:05:30.070] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes 
[2020-04-25 21:05:30.090] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,422
[2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413
[2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312
[2020-04-25 21:05:30.093] [jointLog] [warning] Only 3186382 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 21:05:30.093] [jointLog] [info] Mapping rate = 99.1442%

[2020-04-25 21:05:30.093] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 21:05:30.095] [jointLog] [info] Starting optimizer
[2020-04-25 21:05:30.126] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 21:05:30.137] [jointLog] [info] iteration = 0 | max rel diff. = 7295.51
[2020-04-25 21:05:30.070] [fileLog] [info] 
At end of round 0
==================
Observed 3213886 total fragments (3213886 in most recent round)

[2020-04-25 21:05:30.591] [jointLog] [info] iteration = 100 | max rel diff. = 13.9261
[2020-04-25 21:05:31.055] [jointLog] [info] iteration = 200 | max rel diff. = 0.947747
[2020-04-25 21:05:31.516] [jointLog] [info] iteration = 300 | max rel diff. = 0.331185
[2020-04-25 21:05:31.980] [jointLog] [info] iteration = 400 | max rel diff. = 0.387898
[2020-04-25 21:05:32.446] [jointLog] [info] iteration = 500 | max rel diff. = 0.201543
[2020-04-25 21:05:32.628] [jointLog] [info] iteration = 541 | max rel diff. = 0.00679113
[2020-04-25 21:05:32.630] [jointLog] [info] Finished optimizer
[2020-04-25 21:05:32.630] [jointLog] [info] writing output