[2020-04-26 03:23:20.799] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 03:23:20.799] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 03:23:20.799] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 03:23:20.799] [jointLog] [info] parsing read library format
[2020-04-26 03:23:20.800] [jointLog] [info] There is 1 library.
[2020-04-26 03:23:20.859] [jointLog] [info] Loading pufferfish index
[2020-04-26 03:23:20.859] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 03:23:21.025] [jointLog] [info] done
[2020-04-26 03:23:21.025] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 03:23:21.039] [jointLog] [info] Number of decoys : 0
[2020-04-26 03:23:21.826] [fileLog] [info] 
At end of round 0
==================
Observed 78713 total fragments (78713 in most recent round)

[2020-04-26 03:23:21.826] [jointLog] [info] Computed 12,723 rich equivalence classes for further processing
[2020-04-26 03:23:21.826] [jointLog] [info] Counted 75,333 total reads in the equivalence classes 
[2020-04-26 03:23:21.858] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773
[2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953
[2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724
[2020-04-26 03:23:21.861] [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 03:23:21.861] [jointLog] [info] Mapping rate = 95.7059%

[2020-04-26 03:23:21.861] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 03:23:21.862] [jointLog] [info] Starting optimizer
[2020-04-26 03:23:21.874] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 03:23:21.875] [jointLog] [info] iteration = 0 | max rel diff. = 164.855
[2020-04-26 03:23:21.969] [jointLog] [info] iteration = 100 | max rel diff. = 0.0556853
[2020-04-26 03:23:22.023] [jointLog] [info] iteration = 161 | max rel diff. = 0.00154717
[2020-04-26 03:23:22.023] [jointLog] [info] Finished optimizer
[2020-04-26 03:23:22.023] [jointLog] [info] writing output