[2020-04-25 23:43:57.153] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 23:43:57.153] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 23:43:57.153] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 23:43:57.153] [jointLog] [info] parsing read library format
[2020-04-25 23:43:57.153] [jointLog] [info] There is 1 library.
[2020-04-25 23:43:57.211] [jointLog] [info] Loading pufferfish index
[2020-04-25 23:43:57.211] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 23:43:57.386] [jointLog] [info] done
[2020-04-25 23:43:57.386] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 23:43:57.400] [jointLog] [info] Number of decoys : 0
[2020-04-25 23:44:03.970] [jointLog] [info] Computed 73,003 rich equivalence classes for further processing
[2020-04-25 23:44:03.970] [jointLog] [info] Counted 2,278,267 total reads in the equivalence classes 
[2020-04-25 23:44:03.987] [jointLog] [info] Number of mappings discarded because of alignment score : 461,143
[2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,738
[2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352
[2020-04-25 23:44:03.990] [jointLog] [warning] Only 2278267 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 23:44:03.990] [jointLog] [info] Mapping rate = 99.1405%

[2020-04-25 23:44:03.990] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 23:44:03.992] [jointLog] [info] Starting optimizer
[2020-04-25 23:44:04.013] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 23:44:04.017] [jointLog] [info] iteration = 0 | max rel diff. = 5253.93
[2020-04-25 23:44:04.302] [jointLog] [info] iteration = 100 | max rel diff. = 4.03124
[2020-04-25 23:44:03.970] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-25 23:44:04.580] [jointLog] [info] iteration = 200 | max rel diff. = 1.49539
[2020-04-25 23:44:04.853] [jointLog] [info] iteration = 300 | max rel diff. = 4.77244
[2020-04-25 23:44:05.124] [jointLog] [info] iteration = 400 | max rel diff. = 0.389465
[2020-04-25 23:44:05.402] [jointLog] [info] iteration = 500 | max rel diff. = 0.111154
[2020-04-25 23:44:05.677] [jointLog] [info] iteration = 600 | max rel diff. = 0.182056
[2020-04-25 23:44:05.947] [jointLog] [info] iteration = 700 | max rel diff. = 0.0837297
[2020-04-25 23:44:06.220] [jointLog] [info] iteration = 800 | max rel diff. = 0.0611069
[2020-04-25 23:44:06.302] [jointLog] [info] iteration = 831 | max rel diff. = 0.00377472
[2020-04-25 23:44:06.303] [jointLog] [info] Finished optimizer
[2020-04-25 23:44:06.303] [jointLog] [info] writing output