[2020-04-25 22:22:55.244] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 22:22:55.244] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 22:22:55.244] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 22:22:55.244] [jointLog] [info] parsing read library format
[2020-04-25 22:22:55.244] [jointLog] [info] There is 1 library.
[2020-04-25 22:22:55.306] [jointLog] [info] Loading pufferfish index
[2020-04-25 22:22:55.306] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 22:22:55.394] [jointLog] [info] done
[2020-04-25 22:22:55.394] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 22:22:55.408] [jointLog] [info] Number of decoys : 0
[2020-04-25 22:23:06.009] [jointLog] [info] Computed 95,726 rich equivalence classes for further processing
[2020-04-25 22:23:06.009] [jointLog] [info] Counted 3,196,425 total reads in the equivalence classes 
[2020-04-25 22:23:06.031] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,608
[2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,486
[2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462
[2020-04-25 22:23:06.035] [jointLog] [warning] Only 3196425 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 22:23:06.035] [jointLog] [info] Mapping rate = 99.2016%

[2020-04-25 22:23:06.035] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 22:23:06.037] [jointLog] [info] Starting optimizer
[2020-04-25 22:23:06.063] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 22:23:06.072] [jointLog] [info] iteration = 0 | max rel diff. = 7373.95
[2020-04-25 22:23:06.010] [fileLog] [info] 
At end of round 0
==================
Observed 3222151 total fragments (3222151 in most recent round)

[2020-04-25 22:23:06.455] [jointLog] [info] iteration = 100 | max rel diff. = 16.8416
[2020-04-25 22:23:06.829] [jointLog] [info] iteration = 200 | max rel diff. = 18.6212
[2020-04-25 22:23:07.208] [jointLog] [info] iteration = 300 | max rel diff. = 2.74986
[2020-04-25 22:23:07.584] [jointLog] [info] iteration = 400 | max rel diff. = 0.414992
[2020-04-25 22:23:07.963] [jointLog] [info] iteration = 500 | max rel diff. = 0.151488
[2020-04-25 22:23:08.238] [jointLog] [info] iteration = 574 | max rel diff. = 0.0084751
[2020-04-25 22:23:08.239] [jointLog] [info] Finished optimizer
[2020-04-25 22:23:08.239] [jointLog] [info] writing output