[2023-10-04 19:21:47.855] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 19:21:47.855] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 19:21:47.855] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 19:21:47.855] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 19:21:47.855] [jointLog] [info] parsing read library format
[2023-10-04 19:21:47.855] [jointLog] [info] There is 1 library.
[2023-10-04 19:21:47.856] [jointLog] [info] Loading pufferfish index
[2023-10-04 19:21:47.856] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 19:23:06.417] [jointLog] [info] done
[2023-10-04 19:23:06.570] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 19:23:46.604] [jointLog] [info] Number of decoys : 194
[2023-10-04 19:23:46.624] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 19:23:48.706] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 19:23:49.849] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 19:24:43.631] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-04 19:24:43.654] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-10-04 19:24:43.756] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-10-04 19:24:43.836] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 19:24:43.837] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-04 19:24:43.844] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 19:24:43.906] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 19:24:43.937] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-10-04 19:24:44.124] [jointLog] [info] Computed 83,452 rich equivalence classes for further processing
[2023-10-04 19:24:44.124] [jointLog] [info] Counted 3,416,594 total reads in the equivalence classes 
[2023-10-04 19:24:44.132] [jointLog] [info] Number of mappings discarded because of alignment score : 47,028,442
[2023-10-04 19:24:44.132] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 313,745
[2023-10-04 19:24:44.132] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 86,427
[2023-10-04 19:24:44.132] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 19:24:44.125] [fileLog] [info] 
At end of round 0
==================
Observed 4420336 total fragments (4420336 in most recent round)

[2023-10-04 19:24:45.052] [jointLog] [warning] Only 3416594 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 19:24:45.052] [jointLog] [info] Mapping rate = 77.2926%

[2023-10-04 19:24:45.052] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 19:24:45.053] [jointLog] [info] Starting optimizer
[2023-10-04 19:24:49.756] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 19:24:50.099] [jointLog] [info] iteration = 0 | max rel diff. = 81.8551
[2023-10-04 19:24:53.501] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 19:25:49.085] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 19:25:49.085] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 19:25:53.855] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 19:25:58.821] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 19:26:03.988] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 19:26:09.138] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 19:26:14.134] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 19:26:19.147] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 19:26:23.871] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 19:26:28.969] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 19:26:33.687] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 19:26:38.623] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 19:26:38.625] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 19:27:07.856] [jointLog] [info] iteration = 100 | max rel diff. = 10.2394
[2023-10-04 19:27:39.959] [jointLog] [info] iteration = 200 | max rel diff. = 0.906044
[2023-10-04 19:28:12.061] [jointLog] [info] iteration = 300 | max rel diff. = 16.3425
[2023-10-04 19:28:43.586] [jointLog] [info] iteration = 400 | max rel diff. = 0.0712387
[2023-10-04 19:29:15.223] [jointLog] [info] iteration = 500 | max rel diff. = 0.0332257
[2023-10-04 19:29:46.216] [jointLog] [info] iteration = 600 | max rel diff. = 0.277253
[2023-10-04 19:30:17.495] [jointLog] [info] iteration = 700 | max rel diff. = 0.0209611
[2023-10-04 19:30:48.869] [jointLog] [info] iteration = 800 | max rel diff. = 0.0191562
[2023-10-04 19:31:20.117] [jointLog] [info] iteration = 900 | max rel diff. = 0.804356
[2023-10-04 19:31:26.457] [jointLog] [info] iteration = 921 | max rel diff. = 0.00785978
[2023-10-04 19:31:28.090] [jointLog] [info] Finished optimizer
[2023-10-04 19:31:28.090] [jointLog] [info] writing output