[2020-04-26 02:48:36.456] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 02:48:36.456] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 02:48:36.456] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 02:48:36.456] [jointLog] [info] parsing read library format
[2020-04-26 02:48:36.456] [jointLog] [info] There is 1 library.
[2020-04-26 02:48:36.516] [jointLog] [info] Loading pufferfish index
[2020-04-26 02:48:36.516] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 02:48:36.638] [jointLog] [info] done
[2020-04-26 02:48:36.638] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 02:48:36.652] [jointLog] [info] Number of decoys : 0
[2020-04-26 02:48:42.359] [jointLog] [info] Computed 81,660 rich equivalence classes for further processing
[2020-04-26 02:48:42.359] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes 
[2020-04-26 02:48:42.379] [jointLog] [info] Number of mappings discarded because of alignment score : 733,451
[2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154
[2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582
[2020-04-26 02:48:42.383] [jointLog] [warning] Only 1745454 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 02:48:42.383] [jointLog] [info] Mapping rate = 98.6937%

[2020-04-26 02:48:42.383] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 02:48:42.385] [jointLog] [info] Starting optimizer
[2020-04-26 02:48:42.411] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 02:48:42.416] [jointLog] [info] iteration = 0 | max rel diff. = 3746.67
[2020-04-26 02:48:42.360] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-26 02:48:42.772] [jointLog] [info] iteration = 100 | max rel diff. = 4.45373
[2020-04-26 02:48:43.120] [jointLog] [info] iteration = 200 | max rel diff. = 13.6858
[2020-04-26 02:48:43.465] [jointLog] [info] iteration = 300 | max rel diff. = 0.675412
[2020-04-26 02:48:43.813] [jointLog] [info] iteration = 400 | max rel diff. = 0.0738747
[2020-04-26 02:48:44.166] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218468
[2020-04-26 02:48:44.510] [jointLog] [info] iteration = 600 | max rel diff. = 0.235416
[2020-04-26 02:48:44.530] [jointLog] [info] iteration = 607 | max rel diff. = 0.00447046
[2020-04-26 02:48:44.532] [jointLog] [info] Finished optimizer
[2020-04-26 02:48:44.532] [jointLog] [info] writing output