[2020-04-26 04:43:39.623] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 04:43:39.623] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 04:43:39.623] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 04:43:39.623] [jointLog] [info] parsing read library format
[2020-04-26 04:43:39.623] [jointLog] [info] There is 1 library.
[2020-04-26 04:43:39.685] [jointLog] [info] Loading pufferfish index
[2020-04-26 04:43:39.685] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 04:43:39.835] [jointLog] [info] done
[2020-04-26 04:43:39.835] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 04:43:39.848] [jointLog] [info] Number of decoys : 0
[2020-04-26 04:43:43.629] [fileLog] [info] 
At end of round 0
==================
Observed 1360752 total fragments (1360752 in most recent round)

[2020-04-26 04:43:43.628] [jointLog] [info] Computed 59,737 rich equivalence classes for further processing
[2020-04-26 04:43:43.629] [jointLog] [info] Counted 1,344,958 total reads in the equivalence classes 
[2020-04-26 04:43:43.643] [jointLog] [info] Number of mappings discarded because of alignment score : 339,460
[2020-04-26 04:43:43.643] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,114
[2020-04-26 04:43:43.643] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 04:43:43.643] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,729
[2020-04-26 04:43:43.647] [jointLog] [warning] Only 1344958 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 04:43:43.647] [jointLog] [info] Mapping rate = 98.8393%

[2020-04-26 04:43:43.647] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 04:43:43.648] [jointLog] [info] Starting optimizer
[2020-04-26 04:43:43.669] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 04:43:43.674] [jointLog] [info] iteration = 0 | max rel diff. = 3200.01
[2020-04-26 04:43:43.921] [jointLog] [info] iteration = 100 | max rel diff. = 16.3588
[2020-04-26 04:43:44.166] [jointLog] [info] iteration = 200 | max rel diff. = 0.451516
[2020-04-26 04:43:44.408] [jointLog] [info] iteration = 300 | max rel diff. = 0.0386426
[2020-04-26 04:43:44.649] [jointLog] [info] iteration = 400 | max rel diff. = 0.0376195
[2020-04-26 04:43:44.882] [jointLog] [info] iteration = 500 | max rel diff. = 0.0209438
[2020-04-26 04:43:45.114] [jointLog] [info] iteration = 600 | max rel diff. = 0.0255825
[2020-04-26 04:43:45.192] [jointLog] [info] iteration = 636 | max rel diff. = 0.00829899
[2020-04-26 04:43:45.193] [jointLog] [info] Finished optimizer
[2020-04-26 04:43:45.193] [jointLog] [info] writing output