[2020-04-26 06:47:10.943] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 06:47:10.943] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 06:47:10.943] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 06:47:10.943] [jointLog] [info] parsing read library format
[2020-04-26 06:47:10.943] [jointLog] [info] There is 1 library.
[2020-04-26 06:47:10.996] [jointLog] [info] Loading pufferfish index
[2020-04-26 06:47:10.996] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 06:47:11.248] [jointLog] [info] done
[2020-04-26 06:47:11.248] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 06:47:11.260] [jointLog] [info] Number of decoys : 0
[2020-04-26 06:47:17.940] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-26 06:47:17.939] [jointLog] [info] Computed 72,896 rich equivalence classes for further processing
[2020-04-26 06:47:17.939] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes 
[2020-04-26 06:47:17.956] [jointLog] [info] Number of mappings discarded because of alignment score : 461,126
[2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736
[2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352
[2020-04-26 06:47:17.959] [jointLog] [warning] Only 2278269 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 06:47:17.959] [jointLog] [info] Mapping rate = 99.1406%

[2020-04-26 06:47:17.959] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 06:47:17.961] [jointLog] [info] Starting optimizer
[2020-04-26 06:47:17.983] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 06:47:17.988] [jointLog] [info] iteration = 0 | max rel diff. = 5251.8
[2020-04-26 06:47:18.272] [jointLog] [info] iteration = 100 | max rel diff. = 4.04623
[2020-04-26 06:47:18.553] [jointLog] [info] iteration = 200 | max rel diff. = 0.447318
[2020-04-26 06:47:18.831] [jointLog] [info] iteration = 300 | max rel diff. = 0.569988
[2020-04-26 06:47:19.112] [jointLog] [info] iteration = 400 | max rel diff. = 0.168167
[2020-04-26 06:47:19.387] [jointLog] [info] iteration = 500 | max rel diff. = 19.2218
[2020-04-26 06:47:19.671] [jointLog] [info] iteration = 600 | max rel diff. = 0.201265
[2020-04-26 06:47:19.942] [jointLog] [info] iteration = 700 | max rel diff. = 0.0526721
[2020-04-26 06:47:20.217] [jointLog] [info] iteration = 800 | max rel diff. = 0.11362
[2020-04-26 06:47:20.307] [jointLog] [info] iteration = 833 | max rel diff. = 0.00428601
[2020-04-26 06:47:20.309] [jointLog] [info] Finished optimizer
[2020-04-26 06:47:20.309] [jointLog] [info] writing output