[2020-04-26 01:10:37.407] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 01:10:37.407] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 01:10:37.407] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 01:10:37.407] [jointLog] [info] parsing read library format
[2020-04-26 01:10:37.407] [jointLog] [info] There is 1 library.
[2020-04-26 01:10:37.465] [jointLog] [info] Loading pufferfish index
[2020-04-26 01:10:37.465] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 01:10:37.622] [jointLog] [info] done
[2020-04-26 01:10:37.622] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 01:10:37.636] [jointLog] [info] Number of decoys : 0
[2020-04-26 01:10:39.604] [fileLog] [info] 
At end of round 0
==================
Observed 402112 total fragments (402112 in most recent round)

[2020-04-26 01:10:39.604] [jointLog] [info] Computed 34,296 rich equivalence classes for further processing
[2020-04-26 01:10:39.604] [jointLog] [info] Counted 379,958 total reads in the equivalence classes 
[2020-04-26 01:10:39.638] [jointLog] [info] Number of mappings discarded because of alignment score : 250,107
[2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,667
[2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 899
[2020-04-26 01:10:39.642] [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 01:10:39.642] [jointLog] [info] Mapping rate = 94.4906%

[2020-04-26 01:10:39.642] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 01:10:39.644] [jointLog] [info] Starting optimizer
[2020-04-26 01:10:39.665] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 01:10:39.669] [jointLog] [info] iteration = 0 | max rel diff. = 901.762
[2020-04-26 01:10:39.863] [jointLog] [info] iteration = 100 | max rel diff. = 8.01469
[2020-04-26 01:10:40.051] [jointLog] [info] iteration = 200 | max rel diff. = 0.0667104
[2020-04-26 01:10:40.248] [jointLog] [info] iteration = 300 | max rel diff. = 0.78548
[2020-04-26 01:10:40.440] [jointLog] [info] iteration = 400 | max rel diff. = 0.0839953
[2020-04-26 01:10:40.640] [jointLog] [info] iteration = 500 | max rel diff. = 1.0362
[2020-04-26 01:10:40.669] [jointLog] [info] iteration = 516 | max rel diff. = 0.000648412
[2020-04-26 01:10:40.670] [jointLog] [info] Finished optimizer
[2020-04-26 01:10:40.670] [jointLog] [info] writing output