[2020-04-26 09:42:44.832] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:42:44.832] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:42:44.832] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:42:44.832] [jointLog] [info] parsing read library format
[2020-04-26 09:42:44.832] [jointLog] [info] There is 1 library.
[2020-04-26 09:42:44.893] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:42:44.893] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:42:45.110] [jointLog] [info] done
[2020-04-26 09:42:45.110] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:42:45.124] [jointLog] [info] Number of decoys : 0
[2020-04-26 09:42:50.743] [jointLog] [info] Computed 81,728 rich equivalence classes for further processing
[2020-04-26 09:42:50.743] [jointLog] [info] Counted 1,745,453 total reads in the equivalence classes 
[2020-04-26 09:42:50.764] [jointLog] [info] Number of mappings discarded because of alignment score : 733,454
[2020-04-26 09:42:50.764] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,155
[2020-04-26 09:42:50.764] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 09:42:50.764] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582
[2020-04-26 09:42:50.767] [jointLog] [warning] Only 1745453 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 09:42:50.767] [jointLog] [info] Mapping rate = 98.6937%

[2020-04-26 09:42:50.767] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 09:42:50.769] [jointLog] [info] Starting optimizer
[2020-04-26 09:42:50.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 09:42:50.797] [jointLog] [info] iteration = 0 | max rel diff. = 3746.75
[2020-04-26 09:42:50.744] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-26 09:42:51.155] [jointLog] [info] iteration = 100 | max rel diff. = 3.53085
[2020-04-26 09:42:51.517] [jointLog] [info] iteration = 200 | max rel diff. = 9.51093
[2020-04-26 09:42:51.875] [jointLog] [info] iteration = 300 | max rel diff. = 0.891106
[2020-04-26 09:42:52.230] [jointLog] [info] iteration = 400 | max rel diff. = 0.403766
[2020-04-26 09:42:52.583] [jointLog] [info] iteration = 500 | max rel diff. = 0.119245
[2020-04-26 09:42:52.939] [jointLog] [info] iteration = 600 | max rel diff. = 0.376915
[2020-04-26 09:42:52.953] [jointLog] [info] iteration = 605 | max rel diff. = 0.00443024
[2020-04-26 09:42:52.954] [jointLog] [info] Finished optimizer
[2020-04-26 09:42:52.954] [jointLog] [info] writing output