[2020-04-26 08:56:41.570] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 08:56:41.570] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 08:56:41.570] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 08:56:41.570] [jointLog] [info] parsing read library format
[2020-04-26 08:56:41.570] [jointLog] [info] There is 1 library.
[2020-04-26 08:56:41.629] [jointLog] [info] Loading pufferfish index
[2020-04-26 08:56:41.629] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 08:56:41.711] [jointLog] [info] done
[2020-04-26 08:56:41.711] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 08:56:41.725] [jointLog] [info] Number of decoys : 0
[2020-04-26 08:56:45.543] [fileLog] [info] 
At end of round 0
==================
Observed 1320346 total fragments (1320346 in most recent round)

[2020-04-26 08:56:45.542] [jointLog] [info] Computed 70,119 rich equivalence classes for further processing
[2020-04-26 08:56:45.542] [jointLog] [info] Counted 1,295,947 total reads in the equivalence classes 
[2020-04-26 08:56:45.557] [jointLog] [info] Number of mappings discarded because of alignment score : 406,747
[2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,984
[2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002
[2020-04-26 08:56:45.561] [jointLog] [warning] Only 1295947 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 08:56:45.561] [jointLog] [info] Mapping rate = 98.1521%

[2020-04-26 08:56:45.561] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 08:56:45.562] [jointLog] [info] Starting optimizer
[2020-04-26 08:56:45.585] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 08:56:45.588] [jointLog] [info] iteration = 0 | max rel diff. = 3064.49
[2020-04-26 08:56:45.822] [jointLog] [info] iteration = 100 | max rel diff. = 5.76933
[2020-04-26 08:56:46.046] [jointLog] [info] iteration = 200 | max rel diff. = 0.287623
[2020-04-26 08:56:46.276] [jointLog] [info] iteration = 300 | max rel diff. = 0.135179
[2020-04-26 08:56:46.506] [jointLog] [info] iteration = 400 | max rel diff. = 0.942839
[2020-04-26 08:56:46.731] [jointLog] [info] iteration = 500 | max rel diff. = 0.133679
[2020-04-26 08:56:46.951] [jointLog] [info] iteration = 600 | max rel diff. = 0.794518
[2020-04-26 08:56:47.177] [jointLog] [info] iteration = 700 | max rel diff. = 0.012836
[2020-04-26 08:56:47.335] [jointLog] [info] iteration = 769 | max rel diff. = 0.00982565
[2020-04-26 08:56:47.336] [jointLog] [info] Finished optimizer
[2020-04-26 08:56:47.336] [jointLog] [info] writing output