[2020-04-16 21:37:32.894] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:37:32.894] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:37:32.894] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:37:32.894] [jointLog] [info] parsing read library format
[2020-04-16 21:37:32.894] [jointLog] [info] There is 1 library.
[2020-04-16 21:37:32.960] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:37:32.960] [jointLog] [info] Loading dense pufferfish index.
[2020-04-16 21:37:33.256] [jointLog] [info] done
[2020-04-16 21:37:33.256] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:37:33.282] [jointLog] [info] Number of decoys : 0
[2020-04-16 21:39:27.168] [jointLog] [info] Thread saw mini-batch with a maximum of 39.50% zero probability fragments
[2020-04-16 21:39:27.193] [jointLog] [info] Thread saw mini-batch with a maximum of 38.56% zero probability fragments
[2020-04-16 21:39:27.200] [jointLog] [info] Thread saw mini-batch with a maximum of 39.16% zero probability fragments
[2020-04-16 21:39:27.244] [jointLog] [info] Thread saw mini-batch with a maximum of 38.70% zero probability fragments
[2020-04-16 21:39:27.279] [jointLog] [info] Thread saw mini-batch with a maximum of 38.50% zero probability fragments
[2020-04-16 21:39:27.285] [jointLog] [info] Thread saw mini-batch with a maximum of 38.96% zero probability fragments
[2020-04-16 21:39:27.295] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.307] [jointLog] [info] Thread saw mini-batch with a maximum of 39.24% zero probability fragments
[2020-04-16 21:39:27.315] [jointLog] [info] Thread saw mini-batch with a maximum of 38.88% zero probability fragments
[2020-04-16 21:39:27.316] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.335] [jointLog] [info] Thread saw mini-batch with a maximum of 38.68% zero probability fragments
[2020-04-16 21:39:27.341] [jointLog] [info] Thread saw mini-batch with a maximum of 39.16% zero probability fragments
[2020-04-16 21:39:27.342] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.355] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.374] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.384] [jointLog] [info] Thread saw mini-batch with a maximum of 38.74% zero probability fragments
[2020-04-16 21:39:27.387] [jointLog] [info] Thread saw mini-batch with a maximum of 39.10% zero probability fragments
[2020-04-16 21:39:27.403] [jointLog] [info] Thread saw mini-batch with a maximum of 38.18% zero probability fragments
[2020-04-16 21:39:27.428] [jointLog] [info] Thread saw mini-batch with a maximum of 39.36% zero probability fragments
[2020-04-16 21:39:27.428] [jointLog] [info] Thread saw mini-batch with a maximum of 38.78% zero probability fragments
[2020-04-16 21:39:27.441] [jointLog] [info] Thread saw mini-batch with a maximum of 39.44% zero probability fragments
[2020-04-16 21:39:27.448] [jointLog] [info] Thread saw mini-batch with a maximum of 38.58% zero probability fragments
[2020-04-16 21:39:27.459] [jointLog] [info] Thread saw mini-batch with a maximum of 38.66% zero probability fragments
[2020-04-16 21:39:27.469] [jointLog] [info] Thread saw mini-batch with a maximum of 39.36% zero probability fragments
[2020-04-16 21:39:27.490] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.491] [jointLog] [info] Thread saw mini-batch with a maximum of 39.12% zero probability fragments
[2020-04-16 21:39:27.509] [jointLog] [info] Thread saw mini-batch with a maximum of 38.72% zero probability fragments
[2020-04-16 21:39:27.509] [jointLog] [info] Thread saw mini-batch with a maximum of 39.08% zero probability fragments
[2020-04-16 21:39:27.701] [jointLog] [info] Computed 98,842 rich equivalence classes for further processing
[2020-04-16 21:39:27.701] [jointLog] [info] Counted 10,131,977 total reads in the equivalence classes 
[2020-04-16 21:39:27.718] [jointLog] [warning] 1.3183e-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 17.


[2020-04-16 21:39:27.718] [jointLog] [info] Number of mappings discarded because of alignment score : 346,351,652
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,521,101
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 224,049
[2020-04-16 21:39:27.718] [jointLog] [info] Mapping rate = 22.2616%

[2020-04-16 21:39:27.718] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:39:27.720] [jointLog] [info] Starting optimizer
[2020-04-16 21:39:27.747] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:39:27.751] [jointLog] [info] iteration = 0 | max rel diff. = 19848
[2020-04-16 21:39:27.702] [fileLog] [info] 
At end of round 0
==================
Observed 45513236 total fragments (45513236 in most recent round)

[2020-04-16 21:39:28.023] [jointLog] [info] iteration = 100 | max rel diff. = 4.09158
[2020-04-16 21:39:28.265] [jointLog] [info] iteration = 200 | max rel diff. = 0.641741
[2020-04-16 21:39:28.506] [jointLog] [info] iteration = 300 | max rel diff. = 0.115438
[2020-04-16 21:39:28.747] [jointLog] [info] iteration = 400 | max rel diff. = 5.54545
[2020-04-16 21:39:28.987] [jointLog] [info] iteration = 500 | max rel diff. = 0.0476926
[2020-04-16 21:39:29.228] [jointLog] [info] iteration = 600 | max rel diff. = 0.0858241
[2020-04-16 21:39:29.467] [jointLog] [info] iteration = 700 | max rel diff. = 0.0844504
[2020-04-16 21:39:29.707] [jointLog] [info] iteration = 800 | max rel diff. = 0.00492056
[2020-04-16 21:39:29.707] [jointLog] [info] iteration = 801 | max rel diff. = 0.00492056
[2020-04-16 21:39:29.708] [jointLog] [info] Finished optimizer
[2020-04-16 21:39:29.708] [jointLog] [info] writing output