[2020-04-26 10:34:31.906] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 10:34:31.906] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 10:34:31.906] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 10:34:31.906] [jointLog] [info] parsing read library format
[2020-04-26 10:34:31.906] [jointLog] [info] There is 1 library.
[2020-04-26 10:34:31.967] [jointLog] [info] Loading pufferfish index
[2020-04-26 10:34:31.967] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 10:34:32.124] [jointLog] [info] done
[2020-04-26 10:34:32.124] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 10:34:32.137] [jointLog] [info] Number of decoys : 0
[2020-04-26 10:34:36.705] [jointLog] [info] Computed 60,307 rich equivalence classes for further processing
[2020-04-26 10:34:36.705] [jointLog] [info] Counted 1,107,449 total reads in the equivalence classes 
[2020-04-26 10:34:36.726] [jointLog] [info] Number of mappings discarded because of alignment score : 485,229
[2020-04-26 10:34:36.726] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,163
[2020-04-26 10:34:36.726] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 10:34:36.726] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,777
[2020-04-26 10:34:36.730] [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.

[2020-04-26 10:34:36.730] [jointLog] [info] Mapping rate = 98.8795%

[2020-04-26 10:34:36.730] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 10:34:36.732] [jointLog] [info] Starting optimizer
[2020-04-26 10:34:36.751] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 10:34:36.757] [jointLog] [info] iteration = 0 | max rel diff. = 2448.22
[2020-04-26 10:34:36.706] [fileLog] [info] 
At end of round 0
==================
Observed 1119999 total fragments (1119999 in most recent round)

[2020-04-26 10:34:37.060] [jointLog] [info] iteration = 100 | max rel diff. = 0.410453
[2020-04-26 10:34:37.356] [jointLog] [info] iteration = 200 | max rel diff. = 0.857151
[2020-04-26 10:34:37.654] [jointLog] [info] iteration = 300 | max rel diff. = 0.474845
[2020-04-26 10:34:37.953] [jointLog] [info] iteration = 400 | max rel diff. = 0.0489654
[2020-04-26 10:34:38.095] [jointLog] [info] iteration = 449 | max rel diff. = 0.00226722
[2020-04-26 10:34:38.096] [jointLog] [info] Finished optimizer
[2020-04-26 10:34:38.096] [jointLog] [info] writing output