[2020-04-16 22:08:14.372] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 22:08:14.372] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 22:08:14.372] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 22:08:14.372] [jointLog] [info] parsing read library format
[2020-04-16 22:08:14.372] [jointLog] [info] There is 1 library.
[2020-04-16 22:08:14.436] [jointLog] [info] Loading pufferfish index
[2020-04-16 22:08:14.436] [jointLog] [info] Loading dense pufferfish index.
[2020-04-16 22:08:14.691] [jointLog] [info] done
[2020-04-16 22:08:14.692] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 22:08:14.719] [jointLog] [info] Number of decoys : 0
[2020-04-16 22:10:27.897] [jointLog] [info] Thread saw mini-batch with a maximum of 56.46% zero probability fragments
[2020-04-16 22:10:27.904] [jointLog] [info] Thread saw mini-batch with a maximum of 56.68% zero probability fragments
[2020-04-16 22:10:27.909] [jointLog] [info] Thread saw mini-batch with a maximum of 56.26% zero probability fragments
[2020-04-16 22:10:27.909] [jointLog] [info] Thread saw mini-batch with a maximum of 56.80% zero probability fragments
[2020-04-16 22:10:27.940] [jointLog] [info] Thread saw mini-batch with a maximum of 56.86% zero probability fragments
[2020-04-16 22:10:27.940] [jointLog] [info] Thread saw mini-batch with a maximum of 56.58% zero probability fragments
[2020-04-16 22:10:27.966] [jointLog] [info] Thread saw mini-batch with a maximum of 56.52% zero probability fragments
[2020-04-16 22:10:27.974] [jointLog] [info] Thread saw mini-batch with a maximum of 56.18% zero probability fragments
[2020-04-16 22:10:27.974] [jointLog] [info] Thread saw mini-batch with a maximum of 56.32% zero probability fragments
[2020-04-16 22:10:28.004] [jointLog] [info] Thread saw mini-batch with a maximum of 56.68% zero probability fragments
[2020-04-16 22:10:28.021] [jointLog] [info] Thread saw mini-batch with a maximum of 56.32% zero probability fragments
[2020-04-16 22:10:28.080] [jointLog] [info] Thread saw mini-batch with a maximum of 56.66% zero probability fragments
[2020-04-16 22:10:28.106] [jointLog] [info] Thread saw mini-batch with a maximum of 56.96% zero probability fragments
[2020-04-16 22:10:28.112] [jointLog] [info] Thread saw mini-batch with a maximum of 57.42% zero probability fragments
[2020-04-16 22:10:28.152] [jointLog] [info] Thread saw mini-batch with a maximum of 56.48% zero probability fragments
[2020-04-16 22:10:28.179] [jointLog] [info] Thread saw mini-batch with a maximum of 57.18% zero probability fragments
[2020-04-16 22:10:28.218] [jointLog] [info] Thread saw mini-batch with a maximum of 57.06% zero probability fragments
[2020-04-16 22:10:28.231] [jointLog] [info] Thread saw mini-batch with a maximum of 56.20% zero probability fragments
[2020-04-16 22:10:28.233] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.248] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.248] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.258] [jointLog] [info] Thread saw mini-batch with a maximum of 55.92% zero probability fragments
[2020-04-16 22:10:28.290] [jointLog] [info] Thread saw mini-batch with a maximum of 56.40% zero probability fragments
[2020-04-16 22:10:28.312] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.332] [jointLog] [info] Thread saw mini-batch with a maximum of 56.98% zero probability fragments
[2020-04-16 22:10:28.338] [jointLog] [info] Thread saw mini-batch with a maximum of 56.18% zero probability fragments
[2020-04-16 22:10:28.429] [jointLog] [info] Thread saw mini-batch with a maximum of 57.40% zero probability fragments
[2020-04-16 22:10:28.533] [jointLog] [info] Thread saw mini-batch with a maximum of 56.06% zero probability fragments
[2020-04-16 22:10:28.737] [jointLog] [info] Computed 82,020 rich equivalence classes for further processing
[2020-04-16 22:10:28.737] [jointLog] [info] Counted 12,916,812 total reads in the equivalence classes 
[2020-04-16 22:10:28.755] [jointLog] [warning] 1.77852e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 21.


[2020-04-16 22:10:28.755] [jointLog] [info] Number of mappings discarded because of alignment score : 852,377,255
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,465,423
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 241,533
[2020-04-16 22:10:28.755] [jointLog] [info] Mapping rate = 28.716%

[2020-04-16 22:10:28.755] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 22:10:28.757] [jointLog] [info] Starting optimizer
[2020-04-16 22:10:28.784] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 22:10:28.789] [jointLog] [info] iteration = 0 | max rel diff. = 23333.4
[2020-04-16 22:10:28.738] [fileLog] [info] 
At end of round 0
==================
Observed 44981231 total fragments (44981231 in most recent round)

[2020-04-16 22:10:29.100] [jointLog] [info] iteration = 100 | max rel diff. = 4.21723
[2020-04-16 22:10:29.379] [jointLog] [info] iteration = 200 | max rel diff. = 1.22222
[2020-04-16 22:10:29.632] [jointLog] [info] iteration = 300 | max rel diff. = 2.37504
[2020-04-16 22:10:29.881] [jointLog] [info] iteration = 400 | max rel diff. = 0.0471289
[2020-04-16 22:10:30.130] [jointLog] [info] iteration = 500 | max rel diff. = 0.0434021
[2020-04-16 22:10:30.302] [jointLog] [info] iteration = 569 | max rel diff. = 0.00435499
[2020-04-16 22:10:30.303] [jointLog] [info] Finished optimizer
[2020-04-16 22:10:30.303] [jointLog] [info] writing output