[2020-04-26 05:18:03.107] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 05:18:03.107] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 05:18:03.107] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 05:18:03.107] [jointLog] [info] parsing read library format
[2020-04-26 05:18:03.107] [jointLog] [info] There is 1 library.
[2020-04-26 05:18:03.167] [jointLog] [info] Loading pufferfish index
[2020-04-26 05:18:03.167] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 05:18:03.350] [jointLog] [info] done
[2020-04-26 05:18:03.350] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 05:18:03.362] [jointLog] [info] Number of decoys : 0
[2020-04-26 05:18:12.839] [jointLog] [info] Computed 81,663 rich equivalence classes for further processing
[2020-04-26 05:18:12.839] [jointLog] [info] Counted 3,165,463 total reads in the equivalence classes 
[2020-04-26 05:18:12.857] [jointLog] [info] Number of mappings discarded because of alignment score : 937,199
[2020-04-26 05:18:12.857] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,634
[2020-04-26 05:18:12.857] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 05:18:12.857] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,170
[2020-04-26 05:18:12.861] [jointLog] [warning] Only 3165463 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 05:18:12.861] [jointLog] [info] Mapping rate = 99.2286%

[2020-04-26 05:18:12.861] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 05:18:12.862] [jointLog] [info] Starting optimizer
[2020-04-26 05:18:12.894] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 05:18:12.903] [jointLog] [info] iteration = 0 | max rel diff. = 7007
[2020-04-26 05:18:12.840] [fileLog] [info] 
At end of round 0
==================
Observed 3190071 total fragments (3190071 in most recent round)

[2020-04-26 05:18:13.342] [jointLog] [info] iteration = 100 | max rel diff. = 9.24246
[2020-04-26 05:18:13.771] [jointLog] [info] iteration = 200 | max rel diff. = 2.5459
[2020-04-26 05:18:14.210] [jointLog] [info] iteration = 300 | max rel diff. = 1.2465
[2020-04-26 05:18:14.640] [jointLog] [info] iteration = 400 | max rel diff. = 0.855629
[2020-04-26 05:18:15.071] [jointLog] [info] iteration = 500 | max rel diff. = 0.128742
[2020-04-26 05:18:15.488] [jointLog] [info] iteration = 600 | max rel diff. = 0.321824
[2020-04-26 05:18:15.506] [jointLog] [info] iteration = 605 | max rel diff. = 0.00317837
[2020-04-26 05:18:15.508] [jointLog] [info] Finished optimizer
[2020-04-26 05:18:15.508] [jointLog] [info] writing output