[2023-09-26 18:35:12.938] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 18:35:12.938] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 18:35:12.938] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 18:35:12.938] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 18:35:12.938] [jointLog] [info] parsing read library format
[2023-09-26 18:35:12.938] [jointLog] [info] There is 1 library.
[2023-09-26 18:35:12.938] [jointLog] [info] Loading pufferfish index
[2023-09-26 18:35:12.938] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 18:36:33.018] [jointLog] [info] done
[2023-09-26 18:36:33.196] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 18:37:11.179] [jointLog] [info] Number of decoys : 194
[2023-09-26 18:37:11.179] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 18:37:12.777] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 18:37:13.828] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 18:37:47.531] [jointLog] [info] Thread saw mini-batch with a maximum of 2.38% zero probability fragments
[2023-09-26 18:37:47.533] [jointLog] [info] Thread saw mini-batch with a maximum of 2.40% zero probability fragments
[2023-09-26 18:37:47.638] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-26 18:37:47.669] [jointLog] [info] Thread saw mini-batch with a maximum of 2.52% zero probability fragments
[2023-09-26 18:37:47.671] [jointLog] [info] Thread saw mini-batch with a maximum of 2.32% zero probability fragments
[2023-09-26 18:37:47.787] [jointLog] [info] Thread saw mini-batch with a maximum of 2.38% zero probability fragments
[2023-09-26 18:37:47.839] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-09-26 18:37:47.899] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-09-26 18:37:48.093] [jointLog] [info] Computed 81,835 rich equivalence classes for further processing
[2023-09-26 18:37:48.093] [jointLog] [info] Counted 2,349,595 total reads in the equivalence classes 
[2023-09-26 18:37:48.104] [jointLog] [info] Number of mappings discarded because of alignment score : 30,483,053
[2023-09-26 18:37:48.104] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 211,393
[2023-09-26 18:37:48.104] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,329
[2023-09-26 18:37:48.104] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 18:37:48.094] [fileLog] [info] 
At end of round 0
==================
Observed 3008981 total fragments (3008981 in most recent round)

[2023-09-26 18:37:49.072] [jointLog] [warning] Only 2349595 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 18:37:49.072] [jointLog] [info] Mapping rate = 78.0861%

[2023-09-26 18:37:49.072] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 18:37:49.073] [jointLog] [info] Starting optimizer
[2023-09-26 18:37:53.302] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 18:37:53.632] [jointLog] [info] iteration = 0 | max rel diff. = 50.1387
[2023-09-26 18:37:56.924] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 18:38:44.048] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 18:38:44.048] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 18:38:48.186] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 18:38:52.460] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 18:38:57.082] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 18:39:01.574] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 18:39:06.012] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 18:39:10.629] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 18:39:15.087] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 18:39:19.264] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 18:39:23.797] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 18:39:27.730] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 18:39:58.619] [jointLog] [info] iteration = 100 | max rel diff. = 18.2095
[2023-09-26 18:40:32.066] [jointLog] [info] iteration = 200 | max rel diff. = 0.808027
[2023-09-26 18:41:06.899] [jointLog] [info] iteration = 300 | max rel diff. = 0.067033
[2023-09-26 18:41:41.748] [jointLog] [info] iteration = 400 | max rel diff. = 0.138944
[2023-09-26 18:42:15.912] [jointLog] [info] iteration = 500 | max rel diff. = 0.245658
[2023-09-26 18:42:48.918] [jointLog] [info] iteration = 600 | max rel diff. = 0.0179653
[2023-09-26 18:43:22.237] [jointLog] [info] iteration = 700 | max rel diff. = 0.102919
[2023-09-26 18:43:41.975] [jointLog] [info] iteration = 761 | max rel diff. = 0.0037755
[2023-09-26 18:43:43.920] [jointLog] [info] Finished optimizer
[2023-09-26 18:43:43.920] [jointLog] [info] writing output