[2023-09-25 14:17:49.812] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 14:17:49.812] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 14:17:49.812] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 14:17:49.812] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 14:17:49.812] [jointLog] [info] parsing read library format
[2023-09-25 14:17:49.812] [jointLog] [info] There is 1 library.
[2023-09-25 14:17:49.812] [jointLog] [info] Loading pufferfish index
[2023-09-25 14:17:49.813] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 14:19:09.347] [jointLog] [info] done
[2023-09-25 14:19:09.531] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 14:19:52.006] [jointLog] [info] Number of decoys : 194
[2023-09-25 14:19:52.006] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 14:19:54.026] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 14:19:55.218] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 14:20:32.290] [jointLog] [info] Thread saw mini-batch with a maximum of 4.28% zero probability fragments
[2023-09-25 14:20:32.401] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-09-25 14:20:32.421] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-25 14:20:32.437] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-25 14:20:32.464] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-25 14:20:32.561] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2023-09-25 14:20:32.599] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-25 14:20:32.929] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-25 14:20:33.091] [jointLog] [info] Computed 75,691 rich equivalence classes for further processing
[2023-09-25 14:20:33.091] [jointLog] [info] Counted 2,095,738 total reads in the equivalence classes 
[2023-09-25 14:20:33.100] [jointLog] [info] Number of mappings discarded because of alignment score : 45,645,395
[2023-09-25 14:20:33.100] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 267,558
[2023-09-25 14:20:33.100] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 70,277
[2023-09-25 14:20:33.100] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 14:20:33.092] [fileLog] [info] 
At end of round 0
==================
Observed 2751412 total fragments (2751412 in most recent round)

[2023-09-25 14:20:34.247] [jointLog] [warning] Only 2095738 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-25 14:20:34.247] [jointLog] [info] Mapping rate = 76.1695%

[2023-09-25 14:20:34.247] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 14:20:34.328] [jointLog] [info] Starting optimizer
[2023-09-25 14:21:18.930] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 14:21:19.242] [jointLog] [info] iteration = 0 | max rel diff. = 43.348
[2023-09-25 14:21:22.559] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 14:22:13.279] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 14:22:13.280] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 14:22:17.876] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 14:22:22.510] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 14:22:27.362] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 14:22:32.279] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 14:22:37.073] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 14:22:42.209] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 14:22:46.626] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 14:22:51.218] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 14:22:55.850] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 14:23:01.109] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 14:23:31.927] [jointLog] [info] iteration = 100 | max rel diff. = 9.88938
[2023-09-25 14:24:04.580] [jointLog] [info] iteration = 200 | max rel diff. = 7.60116
[2023-09-25 14:24:37.120] [jointLog] [info] iteration = 300 | max rel diff. = 4.87121
[2023-09-25 14:25:09.748] [jointLog] [info] iteration = 400 | max rel diff. = 0.412048
[2023-09-25 14:25:42.852] [jointLog] [info] iteration = 500 | max rel diff. = 0.0206154
[2023-09-25 14:26:15.248] [jointLog] [info] iteration = 600 | max rel diff. = 0.0234572
[2023-09-25 14:26:49.581] [jointLog] [info] iteration = 700 | max rel diff. = 0.482468
[2023-09-25 14:27:05.410] [jointLog] [info] iteration = 748 | max rel diff. = 0.00659218
[2023-09-25 14:27:08.000] [jointLog] [info] Finished optimizer
[2023-09-25 14:27:08.000] [jointLog] [info] writing output