[2023-08-27 20:19:07.606] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 20:19:07.606] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 20:19:07.606] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 20:19:07.606] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 20:19:07.606] [jointLog] [info] parsing read library format
[2023-08-27 20:19:07.606] [jointLog] [info] There is 1 library.
[2023-08-27 20:19:07.606] [jointLog] [info] Loading pufferfish index
[2023-08-27 20:19:07.606] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 20:20:21.502] [jointLog] [info] done
[2023-08-27 20:20:21.629] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 20:20:57.901] [jointLog] [info] Number of decoys : 194
[2023-08-27 20:20:57.901] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 20:20:59.431] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-27 20:21:00.898] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-27 20:28:40.473] [jointLog] [info] Thread saw mini-batch with a maximum of 4.38% zero probability fragments
[2023-08-27 20:28:40.706] [jointLog] [info] Thread saw mini-batch with a maximum of 4.62% zero probability fragments
[2023-08-27 20:28:40.887] [jointLog] [info] Thread saw mini-batch with a maximum of 5.10% zero probability fragments
[2023-08-27 20:28:41.089] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-08-27 20:28:41.130] [jointLog] [info] Thread saw mini-batch with a maximum of 4.36% zero probability fragments
[2023-08-27 20:28:41.234] [jointLog] [info] Thread saw mini-batch with a maximum of 4.50% zero probability fragments
[2023-08-27 20:28:41.375] [jointLog] [info] Thread saw mini-batch with a maximum of 5.60% zero probability fragments
[2023-08-27 20:28:41.868] [fileLog] [info] 
At end of round 0
==================
Observed 16958003 total fragments (16958003 in most recent round)

[2023-08-27 20:28:41.590] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2023-08-27 20:28:41.868] [jointLog] [info] Computed 252,773 rich equivalence classes for further processing
[2023-08-27 20:28:41.868] [jointLog] [info] Counted 7,479,655 total reads in the equivalence classes 
[2023-08-27 20:28:41.874] [jointLog] [info] Number of mappings discarded because of alignment score : 683,274,855
[2023-08-27 20:28:41.874] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 6,304,122
[2023-08-27 20:28:41.874] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 390,026
[2023-08-27 20:28:41.874] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-27 20:28:41.874] [jointLog] [info] Mapping rate = 44.1069%

[2023-08-27 20:28:41.874] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 20:28:41.875] [jointLog] [info] Starting optimizer
[2023-08-27 20:28:45.465] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 20:28:45.773] [jointLog] [info] iteration = 0 | max rel diff. = 131.815
[2023-08-27 20:28:48.847] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 20:30:25.216] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 20:30:25.216] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 20:30:33.332] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 20:30:42.298] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 20:30:51.253] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 20:31:00.538] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 20:31:09.340] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 20:31:17.889] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 20:31:26.434] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 20:31:34.944] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 20:31:43.845] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 20:31:52.503] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 20:32:21.267] [jointLog] [info] iteration = 100 | max rel diff. = 10.8921
[2023-08-27 20:32:54.212] [jointLog] [info] iteration = 200 | max rel diff. = 1.05345
[2023-08-27 20:33:27.695] [jointLog] [info] iteration = 300 | max rel diff. = 2.8286
[2023-08-27 20:34:01.189] [jointLog] [info] iteration = 400 | max rel diff. = 3.6076
[2023-08-27 20:34:33.857] [jointLog] [info] iteration = 500 | max rel diff. = 1.18653
[2023-08-27 20:35:06.117] [jointLog] [info] iteration = 600 | max rel diff. = 0.502918
[2023-08-27 20:35:38.702] [jointLog] [info] iteration = 700 | max rel diff. = 0.0556565
[2023-08-27 20:36:11.442] [jointLog] [info] iteration = 800 | max rel diff. = 1.19859
[2023-08-27 20:36:13.334] [jointLog] [info] iteration = 807 | max rel diff. = 0.0057526
[2023-08-27 20:36:15.085] [jointLog] [info] Finished optimizer
[2023-08-27 20:36:15.085] [jointLog] [info] writing output