[2020-04-26 05:52:37.471] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 05:52:37.471] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 05:52:37.471] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 05:52:37.471] [jointLog] [info] parsing read library format
[2020-04-26 05:52:37.471] [jointLog] [info] There is 1 library.
[2020-04-26 05:52:37.529] [jointLog] [info] Loading pufferfish index
[2020-04-26 05:52:37.529] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 05:52:37.705] [jointLog] [info] done
[2020-04-26 05:52:37.705] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 05:52:37.719] [jointLog] [info] Number of decoys : 0
[2020-04-26 05:52:38.534] [fileLog] [info] 
At end of round 0
==================
Observed 78713 total fragments (78713 in most recent round)

[2020-04-26 05:52:38.533] [jointLog] [info] Computed 12,708 rich equivalence classes for further processing
[2020-04-26 05:52:38.533] [jointLog] [info] Counted 75,333 total reads in the equivalence classes 
[2020-04-26 05:52:38.566] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773
[2020-04-26 05:52:38.566] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953
[2020-04-26 05:52:38.566] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 05:52:38.566] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724
[2020-04-26 05:52:38.569] [jointLog] [warning] Only 75333 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 05:52:38.569] [jointLog] [info] Mapping rate = 95.7059%

[2020-04-26 05:52:38.569] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 05:52:38.571] [jointLog] [info] Starting optimizer
[2020-04-26 05:52:38.584] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 05:52:38.587] [jointLog] [info] iteration = 0 | max rel diff. = 146.251
[2020-04-26 05:52:38.681] [jointLog] [info] iteration = 100 | max rel diff. = 0.181568
[2020-04-26 05:52:38.733] [jointLog] [info] iteration = 160 | max rel diff. = 0.00300508
[2020-04-26 05:52:38.733] [jointLog] [info] Finished optimizer
[2020-04-26 05:52:38.733] [jointLog] [info] writing output