[2020-04-16 21:48:00.345] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:48:00.345] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:48:00.345] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:48:00.345] [jointLog] [info] parsing read library format
[2020-04-16 21:48:00.345] [jointLog] [info] There is 1 library.
[2020-04-16 21:48:00.411] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:48:00.411] [jointLog] [info] Loading dense pufferfish index.
[2020-04-16 21:48:00.829] [jointLog] [info] done
[2020-04-16 21:48:00.829] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:48:00.853] [jointLog] [info] Number of decoys : 0
[2020-04-16 21:49:29.345] [jointLog] [info] Thread saw mini-batch with a maximum of 49.52% zero probability fragments
[2020-04-16 21:49:29.345] [jointLog] [info] Thread saw mini-batch with a maximum of 48.86% zero probability fragments
[2020-04-16 21:49:29.346] [jointLog] [info] Thread saw mini-batch with a maximum of 49.24% zero probability fragments
[2020-04-16 21:49:29.361] [jointLog] [info] Thread saw mini-batch with a maximum of 48.10% zero probability fragments
[2020-04-16 21:49:29.396] [jointLog] [info] Thread saw mini-batch with a maximum of 49.16% zero probability fragments
[2020-04-16 21:49:29.406] [jointLog] [info] Thread saw mini-batch with a maximum of 48.50% zero probability fragments
[2020-04-16 21:49:29.419] [jointLog] [info] Thread saw mini-batch with a maximum of 48.20% zero probability fragments
[2020-04-16 21:49:29.435] [jointLog] [info] Thread saw mini-batch with a maximum of 49.48% zero probability fragments
[2020-04-16 21:49:29.446] [jointLog] [info] Thread saw mini-batch with a maximum of 48.34% zero probability fragments
[2020-04-16 21:49:29.446] [jointLog] [info] Thread saw mini-batch with a maximum of 48.50% zero probability fragments
[2020-04-16 21:49:29.485] [jointLog] [info] Thread saw mini-batch with a maximum of 49.56% zero probability fragments
[2020-04-16 21:49:29.487] [jointLog] [info] Thread saw mini-batch with a maximum of 48.70% zero probability fragments
[2020-04-16 21:49:29.487] [jointLog] [info] Thread saw mini-batch with a maximum of 48.38% zero probability fragments
[2020-04-16 21:49:29.509] [jointLog] [info] Thread saw mini-batch with a maximum of 48.24% zero probability fragments
[2020-04-16 21:49:29.514] [jointLog] [info] Thread saw mini-batch with a maximum of 48.48% zero probability fragments
[2020-04-16 21:49:29.520] [jointLog] [info] Thread saw mini-batch with a maximum of 49.32% zero probability fragments
[2020-04-16 21:49:29.522] [jointLog] [info] Thread saw mini-batch with a maximum of 47.60% zero probability fragments
[2020-04-16 21:49:29.530] [jointLog] [info] Thread saw mini-batch with a maximum of 49.24% zero probability fragments
[2020-04-16 21:49:29.541] [jointLog] [info] Thread saw mini-batch with a maximum of 48.52% zero probability fragments
[2020-04-16 21:49:29.555] [jointLog] [info] Thread saw mini-batch with a maximum of 48.30% zero probability fragments
[2020-04-16 21:49:29.565] [jointLog] [info] Thread saw mini-batch with a maximum of 48.72% zero probability fragments
[2020-04-16 21:49:29.573] [jointLog] [info] Thread saw mini-batch with a maximum of 48.24% zero probability fragments
[2020-04-16 21:49:29.602] [jointLog] [info] Thread saw mini-batch with a maximum of 49.50% zero probability fragments
[2020-04-16 21:49:29.602] [jointLog] [info] Thread saw mini-batch with a maximum of 47.56% zero probability fragments
[2020-04-16 21:49:29.606] [jointLog] [info] Thread saw mini-batch with a maximum of 48.64% zero probability fragments
[2020-04-16 21:49:29.609] [jointLog] [info] Thread saw mini-batch with a maximum of 49.10% zero probability fragments
[2020-04-16 21:49:29.626] [jointLog] [info] Thread saw mini-batch with a maximum of 48.04% zero probability fragments
[2020-04-16 21:49:29.667] [jointLog] [info] Thread saw mini-batch with a maximum of 49.20% zero probability fragments
[2020-04-16 21:49:29.858] [jointLog] [info] Computed 83,741 rich equivalence classes for further processing
[2020-04-16 21:49:29.858] [jointLog] [info] Counted 12,258,577 total reads in the equivalence classes 
[2020-04-16 21:49:29.875] [jointLog] [warning] 1.03228e-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 16.


[2020-04-16 21:49:29.875] [jointLog] [info] Number of mappings discarded because of alignment score : 308,851,365
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,468,837
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 246,007
[2020-04-16 21:49:29.875] [jointLog] [info] Mapping rate = 31.6358%

[2020-04-16 21:49:29.875] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:49:29.877] [jointLog] [info] Starting optimizer
[2020-04-16 21:49:29.903] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:49:29.907] [jointLog] [info] iteration = 0 | max rel diff. = 22691.2
[2020-04-16 21:49:29.859] [fileLog] [info] 
At end of round 0
==================
Observed 38749085 total fragments (38749085 in most recent round)

[2020-04-16 21:49:30.186] [jointLog] [info] iteration = 100 | max rel diff. = 19.6926
[2020-04-16 21:49:30.437] [jointLog] [info] iteration = 200 | max rel diff. = 0.16521
[2020-04-16 21:49:30.685] [jointLog] [info] iteration = 300 | max rel diff. = 0.683127
[2020-04-16 21:49:30.930] [jointLog] [info] iteration = 400 | max rel diff. = 0.0950398
[2020-04-16 21:49:31.176] [jointLog] [info] iteration = 500 | max rel diff. = 1.41531
[2020-04-16 21:49:31.422] [jointLog] [info] iteration = 600 | max rel diff. = 0.0672739
[2020-04-16 21:49:31.668] [jointLog] [info] iteration = 700 | max rel diff. = 0.032643
[2020-04-16 21:49:31.914] [jointLog] [info] iteration = 800 | max rel diff. = 0.0295341
[2020-04-16 21:49:32.160] [jointLog] [info] iteration = 900 | max rel diff. = 0.108655
[2020-04-16 21:49:32.253] [jointLog] [info] iteration = 939 | max rel diff. = 0.00369978
[2020-04-16 21:49:32.256] [jointLog] [info] Finished optimizer
[2020-04-16 21:49:32.256] [jointLog] [info] writing output