[2020-04-16 21:58:02.984] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:58:02.984] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:58:02.984] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:58:02.984] [jointLog] [info] parsing read library format
[2020-04-16 21:58:02.985] [jointLog] [info] There is 1 library.
[2020-04-16 21:58:03.048] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:58:03.049] [jointLog] [info] Loading dense pufferfish index.
[2020-04-16 21:58:03.307] [jointLog] [info] done
[2020-04-16 21:58:03.307] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:58:03.332] [jointLog] [info] Number of decoys : 0
[2020-04-16 21:59:42.206] [jointLog] [info] Thread saw mini-batch with a maximum of 43.10% zero probability fragments
[2020-04-16 21:59:42.208] [jointLog] [info] Thread saw mini-batch with a maximum of 43.42% zero probability fragments
[2020-04-16 21:59:42.217] [jointLog] [info] Thread saw mini-batch with a maximum of 42.70% zero probability fragments
[2020-04-16 21:59:42.224] [jointLog] [info] Thread saw mini-batch with a maximum of 42.48% zero probability fragments
[2020-04-16 21:59:42.228] [jointLog] [info] Thread saw mini-batch with a maximum of 43.20% zero probability fragments
[2020-04-16 21:59:42.230] [jointLog] [info] Thread saw mini-batch with a maximum of 43.18% zero probability fragments
[2020-04-16 21:59:42.232] [jointLog] [info] Thread saw mini-batch with a maximum of 43.92% zero probability fragments
[2020-04-16 21:59:42.241] [jointLog] [info] Thread saw mini-batch with a maximum of 42.88% zero probability fragments
[2020-04-16 21:59:42.245] [jointLog] [info] Thread saw mini-batch with a maximum of 42.64% zero probability fragments
[2020-04-16 21:59:42.249] [jointLog] [info] Thread saw mini-batch with a maximum of 42.66% zero probability fragments
[2020-04-16 21:59:42.249] [jointLog] [info] Thread saw mini-batch with a maximum of 43.78% zero probability fragments
[2020-04-16 21:59:42.255] [jointLog] [info] Thread saw mini-batch with a maximum of 42.26% zero probability fragments
[2020-04-16 21:59:42.276] [jointLog] [info] Thread saw mini-batch with a maximum of 42.72% zero probability fragments
[2020-04-16 21:59:42.283] [jointLog] [info] Thread saw mini-batch with a maximum of 43.04% zero probability fragments
[2020-04-16 21:59:42.287] [jointLog] [info] Thread saw mini-batch with a maximum of 43.54% zero probability fragments
[2020-04-16 21:59:42.297] [jointLog] [info] Thread saw mini-batch with a maximum of 42.14% zero probability fragments
[2020-04-16 21:59:42.301] [jointLog] [info] Thread saw mini-batch with a maximum of 42.46% zero probability fragments
[2020-04-16 21:59:42.335] [jointLog] [info] Thread saw mini-batch with a maximum of 43.30% zero probability fragments
[2020-04-16 21:59:42.336] [jointLog] [info] Thread saw mini-batch with a maximum of 42.60% zero probability fragments
[2020-04-16 21:59:42.352] [jointLog] [info] Thread saw mini-batch with a maximum of 42.46% zero probability fragments
[2020-04-16 21:59:42.371] [jointLog] [info] Thread saw mini-batch with a maximum of 42.86% zero probability fragments
[2020-04-16 21:59:42.407] [jointLog] [info] Thread saw mini-batch with a maximum of 42.92% zero probability fragments
[2020-04-16 21:59:42.410] [jointLog] [info] Thread saw mini-batch with a maximum of 43.58% zero probability fragments
[2020-04-16 21:59:42.410] [jointLog] [info] Thread saw mini-batch with a maximum of 42.64% zero probability fragments
[2020-04-16 21:59:42.427] [jointLog] [info] Thread saw mini-batch with a maximum of 43.38% zero probability fragments
[2020-04-16 21:59:42.427] [jointLog] [info] Thread saw mini-batch with a maximum of 42.72% zero probability fragments
[2020-04-16 21:59:42.442] [jointLog] [info] Thread saw mini-batch with a maximum of 42.82% zero probability fragments
[2020-04-16 21:59:42.463] [jointLog] [info] Thread saw mini-batch with a maximum of 43.34% zero probability fragments
[2020-04-16 21:59:42.655] [jointLog] [info] Computed 94,991 rich equivalence classes for further processing
[2020-04-16 21:59:42.655] [jointLog] [info] Counted 10,989,050 total reads in the equivalence classes 
[2020-04-16 21:59:42.672] [jointLog] [warning] 3.21961e-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 19.


[2020-04-16 21:59:42.672] [jointLog] [info] Number of mappings discarded because of alignment score : 324,882,706
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,514,062
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 218,535
[2020-04-16 21:59:42.672] [jointLog] [info] Mapping rate = 23.587%

[2020-04-16 21:59:42.672] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:59:42.674] [jointLog] [info] Starting optimizer
[2020-04-16 21:59:42.655] [fileLog] [info] 
At end of round 0
==================
Observed 46589486 total fragments (46589486 in most recent round)

[2020-04-16 21:59:42.705] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:59:42.710] [jointLog] [info] iteration = 0 | max rel diff. = 20957.7
[2020-04-16 21:59:42.995] [jointLog] [info] iteration = 100 | max rel diff. = 5.56898
[2020-04-16 21:59:43.252] [jointLog] [info] iteration = 200 | max rel diff. = 0.948953
[2020-04-16 21:59:43.503] [jointLog] [info] iteration = 300 | max rel diff. = 1.8391
[2020-04-16 21:59:43.750] [jointLog] [info] iteration = 400 | max rel diff. = 0.0785756
[2020-04-16 21:59:43.997] [jointLog] [info] iteration = 500 | max rel diff. = 0.137425
[2020-04-16 21:59:44.039] [jointLog] [info] iteration = 518 | max rel diff. = 0.00939072
[2020-04-16 21:59:44.040] [jointLog] [info] Finished optimizer
[2020-04-16 21:59:44.040] [jointLog] [info] writing output