[2020-04-26 03:06:01.010] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 03:06:01.010] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 03:06:01.010] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 03:06:01.010] [jointLog] [info] parsing read library format
[2020-04-26 03:06:01.010] [jointLog] [info] There is 1 library.
[2020-04-26 03:06:01.070] [jointLog] [info] Loading pufferfish index
[2020-04-26 03:06:01.070] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 03:06:01.239] [jointLog] [info] done
[2020-04-26 03:06:01.239] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 03:06:01.253] [jointLog] [info] Number of decoys : 0
[2020-04-26 03:06:06.237] [jointLog] [info] Computed 53,980 rich equivalence classes for further processing
[2020-04-26 03:06:06.237] [jointLog] [info] Counted 1,453,010 total reads in the equivalence classes 
[2020-04-26 03:06:06.256] [jointLog] [info] Number of mappings discarded because of alignment score : 568,187
[2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,457
[2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,199
[2020-04-26 03:06:06.260] [jointLog] [warning] Only 1453010 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 03:06:06.260] [jointLog] [info] Mapping rate = 98.6031%

[2020-04-26 03:06:06.260] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 03:06:06.262] [jointLog] [info] Starting optimizer
[2020-04-26 03:06:06.279] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 03:06:06.285] [jointLog] [info] iteration = 0 | max rel diff. = 3116.02
[2020-04-26 03:06:06.539] [jointLog] [info] iteration = 100 | max rel diff. = 4.49759
[2020-04-26 03:06:06.237] [fileLog] [info] 
At end of round 0
==================
Observed 1473595 total fragments (1473595 in most recent round)

[2020-04-26 03:06:06.785] [jointLog] [info] iteration = 200 | max rel diff. = 4.80523
[2020-04-26 03:06:07.031] [jointLog] [info] iteration = 300 | max rel diff. = 1.3627
[2020-04-26 03:06:07.282] [jointLog] [info] iteration = 400 | max rel diff. = 0.155924
[2020-04-26 03:06:07.470] [jointLog] [info] iteration = 477 | max rel diff. = 0.00364994
[2020-04-26 03:06:07.471] [jointLog] [info] Finished optimizer
[2020-04-26 03:06:07.471] [jointLog] [info] writing output