[2020-04-26 06:26:55.206] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 06:26:55.206] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 06:26:55.206] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 06:26:55.206] [jointLog] [info] parsing read library format
[2020-04-26 06:26:55.206] [jointLog] [info] There is 1 library.
[2020-04-26 06:26:55.267] [jointLog] [info] Loading pufferfish index
[2020-04-26 06:26:55.267] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 06:26:55.382] [jointLog] [info] done
[2020-04-26 06:26:55.382] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 06:26:55.395] [jointLog] [info] Number of decoys : 0
[2020-04-26 06:26:59.544] [jointLog] [info] Computed 70,009 rich equivalence classes for further processing
[2020-04-26 06:26:59.545] [jointLog] [info] Counted 1,295,947 total reads in the equivalence classes 
[2020-04-26 06:26:59.561] [jointLog] [info] Number of mappings discarded because of alignment score : 406,716
[2020-04-26 06:26:59.561] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,984
[2020-04-26 06:26:59.561] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 06:26:59.561] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002
[2020-04-26 06:26:59.565] [jointLog] [warning] Only 1295947 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 06:26:59.565] [jointLog] [info] Mapping rate = 98.1521%

[2020-04-26 06:26:59.565] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 06:26:59.566] [jointLog] [info] Starting optimizer
[2020-04-26 06:26:59.586] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 06:26:59.590] [jointLog] [info] iteration = 0 | max rel diff. = 3060.97
[2020-04-26 06:26:59.545] [fileLog] [info] 
At end of round 0
==================
Observed 1320346 total fragments (1320346 in most recent round)

[2020-04-26 06:26:59.833] [jointLog] [info] iteration = 100 | max rel diff. = 17.6124
[2020-04-26 06:27:00.073] [jointLog] [info] iteration = 200 | max rel diff. = 0.646969
[2020-04-26 06:27:00.314] [jointLog] [info] iteration = 300 | max rel diff. = 0.52531
[2020-04-26 06:27:00.555] [jointLog] [info] iteration = 400 | max rel diff. = 0.591134
[2020-04-26 06:27:00.790] [jointLog] [info] iteration = 500 | max rel diff. = 0.112025
[2020-04-26 06:27:00.920] [jointLog] [info] iteration = 555 | max rel diff. = 0.0096575
[2020-04-26 06:27:00.921] [jointLog] [info] Finished optimizer
[2020-04-26 06:27:00.921] [jointLog] [info] writing output