[2020-04-26 11:37:49.923] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 11:37:49.923] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 11:37:49.923] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 11:37:49.923] [jointLog] [info] parsing read library format
[2020-04-26 11:37:49.923] [jointLog] [info] There is 1 library.
[2020-04-26 11:37:49.985] [jointLog] [info] Loading pufferfish index
[2020-04-26 11:37:49.985] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 11:37:50.413] [jointLog] [info] done
[2020-04-26 11:37:50.413] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 11:37:50.435] [jointLog] [info] Number of decoys : 0
[2020-04-26 11:37:57.316] [jointLog] [info] Computed 73,272 rich equivalence classes for further processing
[2020-04-26 11:37:57.316] [jointLog] [info] Counted 2,278,268 total reads in the equivalence classes 
[2020-04-26 11:37:57.335] [jointLog] [info] Number of mappings discarded because of alignment score : 461,143
[2020-04-26 11:37:57.335] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,737
[2020-04-26 11:37:57.335] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 11:37:57.335] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352
[2020-04-26 11:37:57.339] [jointLog] [warning] Only 2278268 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 11:37:57.339] [jointLog] [info] Mapping rate = 99.1405%

[2020-04-26 11:37:57.339] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 11:37:57.340] [jointLog] [info] Starting optimizer
[2020-04-26 11:37:57.358] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 11:37:57.363] [jointLog] [info] iteration = 0 | max rel diff. = 5253.99
[2020-04-26 11:37:57.316] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-26 11:37:57.637] [jointLog] [info] iteration = 100 | max rel diff. = 11.8398
[2020-04-26 11:37:57.905] [jointLog] [info] iteration = 200 | max rel diff. = 2.50942
[2020-04-26 11:37:58.186] [jointLog] [info] iteration = 300 | max rel diff. = 0.399247
[2020-04-26 11:37:58.462] [jointLog] [info] iteration = 400 | max rel diff. = 0.115432
[2020-04-26 11:37:58.738] [jointLog] [info] iteration = 500 | max rel diff. = 0.181681
[2020-04-26 11:37:59.014] [jointLog] [info] iteration = 600 | max rel diff. = 0.0778104
[2020-04-26 11:37:59.296] [jointLog] [info] iteration = 700 | max rel diff. = 0.049893
[2020-04-26 11:37:59.571] [jointLog] [info] iteration = 800 | max rel diff. = 15.5198
[2020-04-26 11:37:59.667] [jointLog] [info] iteration = 835 | max rel diff. = 0.0036958
[2020-04-26 11:37:59.669] [jointLog] [info] Finished optimizer
[2020-04-26 11:37:59.669] [jointLog] [info] writing output