[2023-10-04 12:22:10.449] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 12:22:10.449] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 12:22:10.449] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 12:22:10.449] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 12:22:10.449] [jointLog] [info] parsing read library format
[2023-10-04 12:22:10.449] [jointLog] [info] There is 1 library.
[2023-10-04 12:22:10.450] [jointLog] [info] Loading pufferfish index
[2023-10-04 12:22:10.450] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 12:23:40.424] [jointLog] [info] done
[2023-10-04 12:23:40.605] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 12:24:25.125] [jointLog] [info] Number of decoys : 194
[2023-10-04 12:24:25.125] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 12:24:27.438] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 12:24:28.556] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 12:25:10.090] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-10-04 12:25:10.124] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-04 12:25:10.225] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-04 12:25:10.347] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 12:25:10.392] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-04 12:25:10.411] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 12:25:10.527] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-04 12:25:10.562] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 12:25:10.813] [fileLog] [info] 
At end of round 0
==================
Observed 2618646 total fragments (2618646 in most recent round)

[2023-10-04 12:25:10.812] [jointLog] [info] Computed 65,897 rich equivalence classes for further processing
[2023-10-04 12:25:10.812] [jointLog] [info] Counted 1,994,396 total reads in the equivalence classes 
[2023-10-04 12:25:10.819] [jointLog] [info] Number of mappings discarded because of alignment score : 33,695,905
[2023-10-04 12:25:10.819] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 199,535
[2023-10-04 12:25:10.819] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 68,327
[2023-10-04 12:25:10.819] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 12:25:12.365] [jointLog] [warning] Only 1994396 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 12:25:12.365] [jointLog] [info] Mapping rate = 76.1613%

[2023-10-04 12:25:12.365] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 12:25:12.365] [jointLog] [info] Starting optimizer
[2023-10-04 12:25:17.347] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 12:25:17.698] [jointLog] [info] iteration = 0 | max rel diff. = 48.975
[2023-10-04 12:25:21.156] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 12:26:10.321] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 12:26:10.322] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 12:26:14.736] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 12:26:19.313] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 12:26:23.793] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 12:26:28.145] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 12:26:32.695] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 12:26:37.267] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 12:26:41.570] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 12:26:46.354] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 12:26:50.786] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 12:26:55.256] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 12:27:25.827] [jointLog] [info] iteration = 100 | max rel diff. = 3.94842
[2023-10-04 12:28:00.276] [jointLog] [info] iteration = 200 | max rel diff. = 2.63771
[2023-10-04 12:28:34.323] [jointLog] [info] iteration = 300 | max rel diff. = 0.325534
[2023-10-04 12:29:07.690] [jointLog] [info] iteration = 400 | max rel diff. = 0.0200099
[2023-10-04 12:29:41.230] [jointLog] [info] iteration = 500 | max rel diff. = 0.0850581
[2023-10-04 12:30:14.946] [jointLog] [info] iteration = 600 | max rel diff. = 0.0411784
[2023-10-04 12:30:49.006] [jointLog] [info] iteration = 700 | max rel diff. = 0.05787
[2023-10-04 12:31:22.683] [jointLog] [info] iteration = 800 | max rel diff. = 0.110717
[2023-10-04 12:31:26.359] [jointLog] [info] iteration = 812 | max rel diff. = 0.00702059
[2023-10-04 12:31:28.849] [jointLog] [info] Finished optimizer
[2023-10-04 12:31:28.849] [jointLog] [info] writing output