[2020-04-25 21:48:31.230] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 21:48:31.230] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 21:48:31.230] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 21:48:31.230] [jointLog] [info] parsing read library format
[2020-04-25 21:48:31.230] [jointLog] [info] There is 1 library.
[2020-04-25 21:48:31.291] [jointLog] [info] Loading pufferfish index
[2020-04-25 21:48:31.291] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 21:48:31.375] [jointLog] [info] done
[2020-04-25 21:48:31.375] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 21:48:31.389] [jointLog] [info] Number of decoys : 0
[2020-04-25 21:48:34.041] [jointLog] [info] Computed 61,194 rich equivalence classes for further processing
[2020-04-25 21:48:34.041] [jointLog] [info] Counted 792,532 total reads in the equivalence classes 
[2020-04-25 21:48:34.059] [jointLog] [info] Number of mappings discarded because of alignment score : 329,168
[2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,419
[2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,914
[2020-04-25 21:48:34.062] [jointLog] [warning] Only 792532 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 21:48:34.062] [jointLog] [info] Mapping rate = 97.2166%

[2020-04-25 21:48:34.062] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 21:48:34.064] [jointLog] [info] Starting optimizer
[2020-04-25 21:48:34.084] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 21:48:34.088] [jointLog] [info] iteration = 0 | max rel diff. = 1897.92
[2020-04-25 21:48:34.042] [fileLog] [info] 
At end of round 0
==================
Observed 815223 total fragments (815223 in most recent round)

[2020-04-25 21:48:34.316] [jointLog] [info] iteration = 100 | max rel diff. = 0.659093
[2020-04-25 21:48:34.539] [jointLog] [info] iteration = 200 | max rel diff. = 7.7275
[2020-04-25 21:48:34.765] [jointLog] [info] iteration = 300 | max rel diff. = 0.0121327
[2020-04-25 21:48:34.983] [jointLog] [info] iteration = 400 | max rel diff. = 0.00540614
[2020-04-25 21:48:34.984] [jointLog] [info] Finished optimizer
[2020-04-25 21:48:34.984] [jointLog] [info] writing output