[2020-04-26 12:55:38.980] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 12:55:38.980] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 12:55:38.980] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 12:55:38.980] [jointLog] [info] parsing read library format
[2020-04-26 12:55:38.980] [jointLog] [info] There is 1 library.
[2020-04-26 12:55:39.046] [jointLog] [info] Loading pufferfish index
[2020-04-26 12:55:39.046] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 12:55:39.164] [jointLog] [info] done
[2020-04-26 12:55:39.164] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 12:55:39.177] [jointLog] [info] Number of decoys : 0
[2020-04-26 12:55:47.913] [fileLog] [info] 
At end of round 0
==================
Observed 3190071 total fragments (3190071 in most recent round)

[2020-04-26 12:55:47.912] [jointLog] [info] Computed 81,519 rich equivalence classes for further processing
[2020-04-26 12:55:47.912] [jointLog] [info] Counted 3,165,462 total reads in the equivalence classes 
[2020-04-26 12:55:47.932] [jointLog] [info] Number of mappings discarded because of alignment score : 937,179
[2020-04-26 12:55:47.932] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,635
[2020-04-26 12:55:47.932] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 12:55:47.932] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,170
[2020-04-26 12:55:47.936] [jointLog] [warning] Only 3165462 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 12:55:47.936] [jointLog] [info] Mapping rate = 99.2286%

[2020-04-26 12:55:47.936] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 12:55:47.937] [jointLog] [info] Starting optimizer
[2020-04-26 12:55:47.960] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 12:55:47.970] [jointLog] [info] iteration = 0 | max rel diff. = 7007.25
[2020-04-26 12:55:48.396] [jointLog] [info] iteration = 100 | max rel diff. = 10.0822
[2020-04-26 12:55:48.825] [jointLog] [info] iteration = 200 | max rel diff. = 1.57571
[2020-04-26 12:55:49.250] [jointLog] [info] iteration = 300 | max rel diff. = 0.089005
[2020-04-26 12:55:49.675] [jointLog] [info] iteration = 400 | max rel diff. = 0.203039
[2020-04-26 12:55:50.103] [jointLog] [info] iteration = 500 | max rel diff. = 0.0345037
[2020-04-26 12:55:50.456] [jointLog] [info] iteration = 584 | max rel diff. = 0.00287095
[2020-04-26 12:55:50.460] [jointLog] [info] Finished optimizer
[2020-04-26 12:55:50.460] [jointLog] [info] writing output