[2020-04-26 09:13:55.807] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:13:55.807] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:13:55.807] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:13:55.807] [jointLog] [info] parsing read library format
[2020-04-26 09:13:55.807] [jointLog] [info] There is 1 library.
[2020-04-26 09:13:55.859] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:13:55.859] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:13:56.019] [jointLog] [info] done
[2020-04-26 09:13:56.019] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:13:56.030] [jointLog] [info] Number of decoys : 0
[2020-04-26 09:13:57.188] [jointLog] [info] Computed 8,743 rich equivalence classes for further processing
[2020-04-26 09:13:57.188] [jointLog] [info] Counted 91,344 total reads in the equivalence classes 
[2020-04-26 09:13:57.206] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787
[2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280
[2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518
[2020-04-26 09:13:57.209] [jointLog] [warning] Only 91344 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 09:13:57.209] [jointLog] [info] Mapping rate = 89.7518%

[2020-04-26 09:13:57.209] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 09:13:57.211] [jointLog] [info] Starting optimizer
[2020-04-26 09:13:57.224] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 09:13:57.227] [jointLog] [info] iteration = 0 | max rel diff. = 223.38
[2020-04-26 09:13:57.319] [jointLog] [info] iteration = 100 | max rel diff. = 0.16251
[2020-04-26 09:13:57.378] [jointLog] [info] iteration = 170 | max rel diff. = 0.007471
[2020-04-26 09:13:57.379] [jointLog] [info] Finished optimizer
[2020-04-26 09:13:57.379] [jointLog] [info] writing output 

[2020-04-26 09:13:57.188] [fileLog] [info] 
At end of round 0
==================
Observed 101774 total fragments (101774 in most recent round)