[2020-04-25 23:23:08.914] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 23:23:08.914] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 23:23:08.914] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 23:23:08.914] [jointLog] [info] parsing read library format
[2020-04-25 23:23:08.914] [jointLog] [info] There is 1 library.
[2020-04-25 23:23:08.972] [jointLog] [info] Loading pufferfish index
[2020-04-25 23:23:08.973] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 23:23:09.178] [jointLog] [info] done
[2020-04-25 23:23:09.178] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 23:23:09.193] [jointLog] [info] Number of decoys : 0
[2020-04-25 23:23:15.148] [jointLog] [info] Computed 63,989 rich equivalence classes for further processing
[2020-04-25 23:23:15.148] [jointLog] [info] Counted 1,547,156 total reads in the equivalence classes 
[2020-04-25 23:23:15.169] [jointLog] [info] Number of mappings discarded because of alignment score : 744,608
[2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,255
[2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,061
[2020-04-25 23:23:15.173] [jointLog] [warning] Only 1547156 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 23:23:15.173] [jointLog] [info] Mapping rate = 98.6772%

[2020-04-25 23:23:15.173] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 23:23:15.174] [jointLog] [info] Starting optimizer
[2020-04-25 23:23:15.197] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 23:23:15.204] [jointLog] [info] iteration = 0 | max rel diff. = 3445.26
[2020-04-25 23:23:15.534] [jointLog] [info] iteration = 100 | max rel diff. = 1.74427
[2020-04-25 23:23:15.148] [fileLog] [info] 
At end of round 0
==================
Observed 1567896 total fragments (1567896 in most recent round)

[2020-04-25 23:23:15.857] [jointLog] [info] iteration = 200 | max rel diff. = 2.34535
[2020-04-25 23:23:16.181] [jointLog] [info] iteration = 300 | max rel diff. = 0.0146923
[2020-04-25 23:23:16.507] [jointLog] [info] iteration = 400 | max rel diff. = 0.0433253
[2020-04-25 23:23:16.831] [jointLog] [info] iteration = 500 | max rel diff. = 0.0212253
[2020-04-25 23:23:16.973] [jointLog] [info] iteration = 544 | max rel diff. = 0.00267322
[2020-04-25 23:23:16.974] [jointLog] [info] Finished optimizer
[2020-04-25 23:23:16.974] [jointLog] [info] writing output