[2020-04-26 06:01:09.216] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 06:01:09.216] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 06:01:09.216] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 06:01:09.216] [jointLog] [info] parsing read library format
[2020-04-26 06:01:09.216] [jointLog] [info] There is 1 library.
[2020-04-26 06:01:09.278] [jointLog] [info] Loading pufferfish index
[2020-04-26 06:01:09.279] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 06:01:09.367] [jointLog] [info] done
[2020-04-26 06:01:09.367] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 06:01:09.381] [jointLog] [info] Number of decoys : 0
[2020-04-26 06:01:10.141] [fileLog] [info] 
At end of round 0
==================
Observed 56697 total fragments (56697 in most recent round)

[2020-04-26 06:01:10.140] [jointLog] [info] Computed 8,677 rich equivalence classes for further processing
[2020-04-26 06:01:10.140] [jointLog] [info] Counted 49,503 total reads in the equivalence classes 
[2020-04-26 06:01:10.178] [jointLog] [info] Number of mappings discarded because of alignment score : 49,151
[2020-04-26 06:01:10.178] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,787
[2020-04-26 06:01:10.178] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 06:01:10.178] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 268
[2020-04-26 06:01:10.182] [jointLog] [warning] Only 49503 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 06:01:10.182] [jointLog] [info] Mapping rate = 87.3115%

[2020-04-26 06:01:10.182] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 06:01:10.183] [jointLog] [info] Starting optimizer
[2020-04-26 06:01:10.195] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 06:01:10.200] [jointLog] [info] iteration = 0 | max rel diff. = 119.457
[2020-04-26 06:01:10.278] [jointLog] [info] iteration = 100 | max rel diff. = 0.357938
[2020-04-26 06:01:10.306] [jointLog] [info] iteration = 142 | max rel diff. = 0.00891147
[2020-04-26 06:01:10.307] [jointLog] [info] Finished optimizer
[2020-04-26 06:01:10.307] [jointLog] [info] writing output