[2023-09-28 12:37:45.189] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 12:37:45.189] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 12:37:45.189] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 12:37:45.189] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 12:37:45.189] [jointLog] [info] parsing read library format
[2023-09-28 12:37:45.189] [jointLog] [info] There is 1 library.
[2023-09-28 12:37:45.189] [jointLog] [info] Loading pufferfish index
[2023-09-28 12:37:45.189] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 12:38:59.042] [jointLog] [info] done
[2023-09-28 12:38:59.167] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 12:39:34.462] [jointLog] [info] Number of decoys : 194
[2023-09-28 12:39:34.462] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 12:39:35.486] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 12:39:36.754] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 12:40:07.910] [jointLog] [info] Thread saw mini-batch with a maximum of 9.09% zero probability fragments
[2023-09-28 12:40:07.930] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-28 12:40:07.948] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-28 12:40:07.965] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-28 12:40:08.049] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-28 12:40:08.108] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-28 12:40:08.257] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-28 12:40:08.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-28 12:40:08.526] [jointLog] [info] Computed 80,013 rich equivalence classes for further processing
[2023-09-28 12:40:08.526] [jointLog] [info] Counted 1,905,453 total reads in the equivalence classes 
[2023-09-28 12:40:08.532] [jointLog] [warning] 0.000121457% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 10.


[2023-09-28 12:40:08.532] [jointLog] [info] Number of mappings discarded because of alignment score : 35,397,402
[2023-09-28 12:40:08.532] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 201,954
[2023-09-28 12:40:08.532] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 60,964
[2023-09-28 12:40:08.532] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 12:40:08.527] [fileLog] [info] 
At end of round 0
==================
Observed 2470011 total fragments (2470011 in most recent round)

[2023-09-28 12:40:09.222] [jointLog] [warning] Only 1905453 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-28 12:40:09.222] [jointLog] [info] Mapping rate = 77.1435%

[2023-09-28 12:40:09.222] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 12:40:09.223] [jointLog] [info] Starting optimizer
[2023-09-28 12:40:12.897] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 12:40:13.233] [jointLog] [info] iteration = 0 | max rel diff. = 38.6497
[2023-09-28 12:40:16.635] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 12:41:13.069] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 12:41:13.069] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 12:41:18.013] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 12:41:23.026] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 12:41:28.325] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 12:41:33.576] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 12:41:38.710] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 12:41:44.005] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 12:41:49.163] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 12:41:54.235] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 12:41:59.170] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 12:42:04.169] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 12:42:33.891] [jointLog] [info] iteration = 100 | max rel diff. = 1.77988
[2023-09-28 12:43:05.692] [jointLog] [info] iteration = 200 | max rel diff. = 2.32821
[2023-09-28 12:43:37.244] [jointLog] [info] iteration = 300 | max rel diff. = 0.740429
[2023-09-28 12:44:11.082] [jointLog] [info] iteration = 400 | max rel diff. = 0.186574
[2023-09-28 12:44:44.688] [jointLog] [info] iteration = 500 | max rel diff. = 0.185408
[2023-09-28 12:45:18.610] [jointLog] [info] iteration = 600 | max rel diff. = 0.430746
[2023-09-28 12:45:52.869] [jointLog] [info] iteration = 700 | max rel diff. = 0.0559569
[2023-09-28 12:46:00.613] [jointLog] [info] iteration = 724 | max rel diff. = 0.00877911
[2023-09-28 12:46:02.410] [jointLog] [info] Finished optimizer
[2023-09-28 12:46:02.410] [jointLog] [info] writing output