[2020-04-26 00:53:23.043] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 00:53:23.043] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 00:53:23.043] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 00:53:23.043] [jointLog] [info] parsing read library format
[2020-04-26 00:53:23.043] [jointLog] [info] There is 1 library.
[2020-04-26 00:53:23.101] [jointLog] [info] Loading pufferfish index
[2020-04-26 00:53:23.101] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 00:53:23.223] [jointLog] [info] done
[2020-04-26 00:53:23.223] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 00:53:23.237] [jointLog] [info] Number of decoys : 0
[2020-04-26 00:53:27.165] [fileLog] [info] 
At end of round 0
==================
Observed 1360752 total fragments (1360752 in most recent round)

[2020-04-26 00:53:27.164] [jointLog] [info] Computed 59,979 rich equivalence classes for further processing
[2020-04-26 00:53:27.164] [jointLog] [info] Counted 1,344,958 total reads in the equivalence classes 
[2020-04-26 00:53:27.181] [jointLog] [info] Number of mappings discarded because of alignment score : 339,452
[2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,114
[2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,729
[2020-04-26 00:53:27.184] [jointLog] [warning] Only 1344958 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 00:53:27.184] [jointLog] [info] Mapping rate = 98.8393%

[2020-04-26 00:53:27.184] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 00:53:27.187] [jointLog] [info] Starting optimizer
[2020-04-26 00:53:27.212] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 00:53:27.218] [jointLog] [info] iteration = 0 | max rel diff. = 3200.66
[2020-04-26 00:53:27.461] [jointLog] [info] iteration = 100 | max rel diff. = 15.9748
[2020-04-26 00:53:27.694] [jointLog] [info] iteration = 200 | max rel diff. = 0.375802
[2020-04-26 00:53:27.934] [jointLog] [info] iteration = 300 | max rel diff. = 0.0429109
[2020-04-26 00:53:28.169] [jointLog] [info] iteration = 400 | max rel diff. = 0.0190115
[2020-04-26 00:53:28.405] [jointLog] [info] iteration = 500 | max rel diff. = 0.0215478
[2020-04-26 00:53:28.643] [jointLog] [info] iteration = 600 | max rel diff. = 0.0152558
[2020-04-26 00:53:28.878] [jointLog] [info] iteration = 700 | max rel diff. = 0.396061
[2020-04-26 00:53:29.027] [jointLog] [info] iteration = 762 | max rel diff. = 0.0029772
[2020-04-26 00:53:29.028] [jointLog] [info] Finished optimizer
[2020-04-26 00:53:29.028] [jointLog] [info] writing output