[2023-10-03 02:42:03.266] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 02:42:03.267] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 02:42:03.267] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 02:42:03.267] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 02:42:03.267] [jointLog] [info] parsing read library format
[2023-10-03 02:42:03.267] [jointLog] [info] There is 1 library.
[2023-10-03 02:42:03.267] [jointLog] [info] Loading pufferfish index
[2023-10-03 02:42:03.267] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 02:43:17.807] [jointLog] [info] done
[2023-10-03 02:43:17.965] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 02:43:58.278] [jointLog] [info] Number of decoys : 194
[2023-10-03 02:43:58.278] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 02:44:00.197] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 02:44:01.382] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 02:44:45.970] [jointLog] [info] Thread saw mini-batch with a maximum of 3.23% zero probability fragments
[2023-10-03 02:44:46.007] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 02:44:46.187] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-03 02:44:46.260] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-03 02:44:46.305] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 02:44:46.417] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 02:44:46.463] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 02:44:46.476] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-10-03 02:44:46.660] [jointLog] [info] Computed 89,509 rich equivalence classes for further processing
[2023-10-03 02:44:46.660] [jointLog] [info] Counted 2,299,915 total reads in the equivalence classes 
[2023-10-03 02:44:46.668] [jointLog] [info] Number of mappings discarded because of alignment score : 54,630,318
[2023-10-03 02:44:46.669] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 315,007
[2023-10-03 02:44:46.669] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 71,389
[2023-10-03 02:44:46.669] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 02:44:46.661] [fileLog] [info] 
At end of round 0
==================
Observed 3030031 total fragments (3030031 in most recent round)

[2023-10-03 02:44:47.799] [jointLog] [warning] Only 2299915 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 02:44:47.799] [jointLog] [info] Mapping rate = 75.904%

[2023-10-03 02:44:47.799] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 02:44:47.799] [jointLog] [info] Starting optimizer
[2023-10-03 02:44:53.599] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 02:44:53.927] [jointLog] [info] iteration = 0 | max rel diff. = 44.7273
[2023-10-03 02:44:57.203] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 02:45:53.285] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 02:45:53.285] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 02:45:58.408] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 02:46:03.801] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 02:46:08.891] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 02:46:14.498] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 02:46:19.941] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 02:46:25.122] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 02:46:30.163] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 02:46:35.349] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 02:46:40.727] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 02:46:45.682] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 02:47:17.519] [jointLog] [info] iteration = 100 | max rel diff. = 7.75239
[2023-10-03 02:47:51.982] [jointLog] [info] iteration = 200 | max rel diff. = 0.356477
[2023-10-03 02:48:25.598] [jointLog] [info] iteration = 300 | max rel diff. = 9.68502
[2023-10-03 02:48:58.984] [jointLog] [info] iteration = 400 | max rel diff. = 0.232776
[2023-10-03 02:49:32.700] [jointLog] [info] iteration = 500 | max rel diff. = 0.126159
[2023-10-03 02:50:06.262] [jointLog] [info] iteration = 600 | max rel diff. = 0.081045
[2023-10-03 02:50:39.941] [jointLog] [info] iteration = 700 | max rel diff. = 0.0604335
[2023-10-03 02:50:45.993] [jointLog] [info] iteration = 719 | max rel diff. = 0.00958366
[2023-10-03 02:50:47.821] [jointLog] [info] Finished optimizer
[2023-10-03 02:50:47.821] [jointLog] [info] writing output