[2020-04-26 10:51:40.028] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 10:51:40.028] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 10:51:40.028] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 10:51:40.028] [jointLog] [info] parsing read library format
[2020-04-26 10:51:40.028] [jointLog] [info] There is 1 library.
[2020-04-26 10:51:40.088] [jointLog] [info] Loading pufferfish index
[2020-04-26 10:51:40.089] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 10:51:40.222] [jointLog] [info] done
[2020-04-26 10:51:40.222] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 10:51:40.236] [jointLog] [info] Number of decoys : 0
[2020-04-26 10:51:49.030] [fileLog] [info] 
At end of round 0
==================
Observed 3222151 total fragments (3222151 in most recent round)

[2020-04-26 10:51:49.030] [jointLog] [info] Computed 95,462 rich equivalence classes for further processing
[2020-04-26 10:51:49.030] [jointLog] [info] Counted 3,196,425 total reads in the equivalence classes 
[2020-04-26 10:51:49.051] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,610
[2020-04-26 10:51:49.051] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,486
[2020-04-26 10:51:49.051] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 10:51:49.051] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462
[2020-04-26 10:51:49.055] [jointLog] [warning] Only 3196425 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 10:51:49.055] [jointLog] [info] Mapping rate = 99.2016%

[2020-04-26 10:51:49.055] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 10:51:49.057] [jointLog] [info] Starting optimizer
[2020-04-26 10:51:49.083] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 10:51:49.090] [jointLog] [info] iteration = 0 | max rel diff. = 7370.66
[2020-04-26 10:51:49.471] [jointLog] [info] iteration = 100 | max rel diff. = 19.8158
[2020-04-26 10:51:49.844] [jointLog] [info] iteration = 200 | max rel diff. = 5.90281
[2020-04-26 10:51:50.226] [jointLog] [info] iteration = 300 | max rel diff. = 2.63821
[2020-04-26 10:51:50.597] [jointLog] [info] iteration = 400 | max rel diff. = 1.31875
[2020-04-26 10:51:50.973] [jointLog] [info] iteration = 500 | max rel diff. = 0.147327
[2020-04-26 10:51:51.334] [jointLog] [info] iteration = 600 | max rel diff. = 0.0120441
[2020-04-26 10:51:51.695] [jointLog] [info] iteration = 700 | max rel diff. = 0.0392574
[2020-04-26 10:51:52.059] [jointLog] [info] iteration = 800 | max rel diff. = 0.0281628
[2020-04-26 10:51:52.187] [jointLog] [info] iteration = 836 | max rel diff. = 0.00662109
[2020-04-26 10:51:52.190] [jointLog] [info] Finished optimizer
[2020-04-26 10:51:52.190] [jointLog] [info] writing output