[2020-04-25 22:05:47.633] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 22:05:47.633] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 22:05:47.633] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 22:05:47.633] [jointLog] [info] parsing read library format
[2020-04-25 22:05:47.633] [jointLog] [info] There is 1 library.
[2020-04-25 22:05:47.692] [jointLog] [info] Loading pufferfish index
[2020-04-25 22:05:47.692] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 22:05:47.774] [jointLog] [info] done
[2020-04-25 22:05:47.774] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 22:05:47.788] [jointLog] [info] Number of decoys : 0
[2020-04-25 22:05:52.255] [fileLog] [info] 
At end of round 0
==================
Observed 1119999 total fragments (1119999 in most recent round)

[2020-04-25 22:05:52.254] [jointLog] [info] Computed 60,283 rich equivalence classes for further processing
[2020-04-25 22:05:52.254] [jointLog] [info] Counted 1,107,449 total reads in the equivalence classes 
[2020-04-25 22:05:52.273] [jointLog] [info] Number of mappings discarded because of alignment score : 485,229
[2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,163
[2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,777
[2020-04-25 22:05:52.277] [jointLog] [warning] Only 1107449 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 22:05:52.277] [jointLog] [info] Mapping rate = 98.8795%

[2020-04-25 22:05:52.277] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 22:05:52.279] [jointLog] [info] Starting optimizer
[2020-04-25 22:05:52.297] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 22:05:52.302] [jointLog] [info] iteration = 0 | max rel diff. = 2447.97
[2020-04-25 22:05:52.606] [jointLog] [info] iteration = 100 | max rel diff. = 0.344132
[2020-04-25 22:05:52.916] [jointLog] [info] iteration = 200 | max rel diff. = 0.850319
[2020-04-25 22:05:53.222] [jointLog] [info] iteration = 300 | max rel diff. = 0.50341
[2020-04-25 22:05:53.525] [jointLog] [info] iteration = 400 | max rel diff. = 0.277981
[2020-04-25 22:05:53.672] [jointLog] [info] iteration = 449 | max rel diff. = 0.0022278
[2020-04-25 22:05:53.673] [jointLog] [info] Finished optimizer
[2020-04-25 22:05:53.673] [jointLog] [info] writing output