[2020-04-26 07:13:08.714] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 07:13:08.714] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 07:13:08.714] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 07:13:08.714] [jointLog] [info] parsing read library format
[2020-04-26 07:13:08.714] [jointLog] [info] There is 1 library.
[2020-04-26 07:13:08.776] [jointLog] [info] Loading pufferfish index
[2020-04-26 07:13:08.777] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 07:13:08.907] [jointLog] [info] done
[2020-04-26 07:13:08.907] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 07:13:08.921] [jointLog] [info] Number of decoys : 0
[2020-04-26 07:13:20.161] [fileLog] [info] 
At end of round 0
==================
Observed 4311037 total fragments (4311037 in most recent round)

[2020-04-26 07:13:20.160] [jointLog] [info] Computed 99,602 rich equivalence classes for further processing
[2020-04-26 07:13:20.160] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes 
[2020-04-26 07:13:20.179] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,051
[2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025
[2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,877
[2020-04-26 07:13:20.183] [jointLog] [warning] Only 4278214 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 07:13:20.183] [jointLog] [info] Mapping rate = 99.2386%

[2020-04-26 07:13:20.183] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 07:13:20.184] [jointLog] [info] Starting optimizer
[2020-04-26 07:13:20.208] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 07:13:20.220] [jointLog] [info] iteration = 0 | max rel diff. = 9617.12
[2020-04-26 07:13:20.737] [jointLog] [info] iteration = 100 | max rel diff. = 8.28216
[2020-04-26 07:13:21.254] [jointLog] [info] iteration = 200 | max rel diff. = 5.66174
[2020-04-26 07:13:21.771] [jointLog] [info] iteration = 300 | max rel diff. = 0.322196
[2020-04-26 07:13:22.287] [jointLog] [info] iteration = 400 | max rel diff. = 0.597547
[2020-04-26 07:13:22.812] [jointLog] [info] iteration = 500 | max rel diff. = 0.165034
[2020-04-26 07:13:23.331] [jointLog] [info] iteration = 600 | max rel diff. = 0.224161
[2020-04-26 07:13:23.850] [jointLog] [info] iteration = 700 | max rel diff. = 0.0609157
[2020-04-26 07:13:24.368] [jointLog] [info] iteration = 800 | max rel diff. = 0.0650154
[2020-04-26 07:13:24.684] [jointLog] [info] iteration = 862 | max rel diff. = 0.00325945
[2020-04-26 07:13:24.687] [jointLog] [info] Finished optimizer
[2020-04-26 07:13:24.687] [jointLog] [info] writing output