[2023-10-04 20:31:10.104] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 20:31:10.104] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 20:31:10.104] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 20:31:10.104] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 20:31:10.104] [jointLog] [info] parsing read library format
[2023-10-04 20:31:10.104] [jointLog] [info] There is 1 library.
[2023-10-04 20:31:10.104] [jointLog] [info] Loading pufferfish index
[2023-10-04 20:31:10.105] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 20:32:33.657] [jointLog] [info] done
[2023-10-04 20:32:33.796] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 20:33:13.437] [jointLog] [info] Number of decoys : 194
[2023-10-04 20:33:13.437] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 20:33:14.911] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 20:33:17.734] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 20:34:28.075] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-10-04 20:34:28.260] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 20:34:28.290] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 20:34:28.349] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 20:34:28.421] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-10-04 20:34:28.434] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-10-04 20:34:28.476] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 20:34:28.541] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 20:34:28.747] [jointLog] [info] Computed 79,065 rich equivalence classes for further processing
[2023-10-04 20:34:28.747] [jointLog] [info] Counted 3,291,383 total reads in the equivalence classes 
[2023-10-04 20:34:28.756] [jointLog] [info] Number of mappings discarded because of alignment score : 64,061,357
[2023-10-04 20:34:28.756] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 347,688
[2023-10-04 20:34:28.756] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 109,145
[2023-10-04 20:34:28.756] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 20:34:28.748] [fileLog] [info] 
At end of round 0
==================
Observed 4297172 total fragments (4297172 in most recent round)

[2023-10-04 20:34:29.820] [jointLog] [warning] Only 3291383 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 20:34:29.820] [jointLog] [info] Mapping rate = 76.5942%

[2023-10-04 20:34:29.820] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 20:34:29.820] [jointLog] [info] Starting optimizer
[2023-10-04 20:34:34.539] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 20:34:34.925] [jointLog] [info] iteration = 0 | max rel diff. = 73.3875
[2023-10-04 20:34:38.560] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 20:35:42.373] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 20:35:42.374] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 20:35:48.103] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 20:35:54.161] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 20:36:00.964] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 20:36:07.482] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 20:36:14.027] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 20:36:21.232] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 20:36:27.629] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 20:36:33.454] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 20:36:39.467] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 20:36:45.655] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 20:37:17.809] [jointLog] [info] iteration = 100 | max rel diff. = 19.058
[2023-10-04 20:37:54.190] [jointLog] [info] iteration = 200 | max rel diff. = 4.83264
[2023-10-04 20:38:29.807] [jointLog] [info] iteration = 300 | max rel diff. = 0.324569
[2023-10-04 20:39:06.342] [jointLog] [info] iteration = 400 | max rel diff. = 0.646739
[2023-10-04 20:39:42.415] [jointLog] [info] iteration = 500 | max rel diff. = 0.055304
[2023-10-04 20:40:19.147] [jointLog] [info] iteration = 600 | max rel diff. = 0.0617323
[2023-10-04 20:40:56.050] [jointLog] [info] iteration = 700 | max rel diff. = 0.0133811
[2023-10-04 20:41:32.357] [jointLog] [info] iteration = 800 | max rel diff. = 0.0179678
[2023-10-04 20:42:05.766] [jointLog] [info] iteration = 894 | max rel diff. = 0.00628522
[2023-10-04 20:42:07.798] [jointLog] [info] Finished optimizer
[2023-10-04 20:42:07.798] [jointLog] [info] writing output