[2023-09-23 19:31:42.531] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 19:31:42.531] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 19:31:42.531] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 19:31:42.531] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 19:31:42.531] [jointLog] [info] parsing read library format
[2023-09-23 19:31:42.531] [jointLog] [info] There is 1 library.
[2023-09-23 19:31:42.531] [jointLog] [info] Loading pufferfish index
[2023-09-23 19:31:42.531] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 19:33:00.441] [jointLog] [info] done
[2023-09-23 19:33:00.599] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 19:33:40.167] [jointLog] [info] Number of decoys : 194
[2023-09-23 19:33:40.167] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 19:33:42.006] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 19:33:42.931] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 19:34:42.846] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-23 19:34:42.943] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-23 19:34:43.051] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-23 19:34:43.078] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-23 19:34:43.191] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-23 19:34:43.200] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-23 19:34:43.212] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-23 19:34:43.269] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-23 19:34:43.465] [jointLog] [info] Computed 79,952 rich equivalence classes for further processing
[2023-09-23 19:34:43.465] [jointLog] [info] Counted 3,661,894 total reads in the equivalence classes 
[2023-09-23 19:34:43.473] [jointLog] [info] Number of mappings discarded because of alignment score : 57,568,161
[2023-09-23 19:34:43.473] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 427,122
[2023-09-23 19:34:43.473] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 116,998
[2023-09-23 19:34:43.473] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 19:34:43.466] [fileLog] [info] 
At end of round 0
==================
Observed 4683337 total fragments (4683337 in most recent round)

[2023-09-23 19:34:44.681] [jointLog] [warning] Only 3661894 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 19:34:44.681] [jointLog] [info] Mapping rate = 78.1898%

[2023-09-23 19:34:44.681] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 19:34:44.681] [jointLog] [info] Starting optimizer
[2023-09-23 19:34:49.444] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 19:34:49.781] [jointLog] [info] iteration = 0 | max rel diff. = 77.9245
[2023-09-23 19:34:53.129] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 19:35:50.792] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 19:35:50.793] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 19:35:56.410] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 19:36:01.256] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 19:36:06.963] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 19:36:12.469] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 19:36:17.866] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 19:36:23.106] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 19:36:28.102] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 19:36:33.147] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 19:36:38.777] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 19:36:44.420] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 19:37:16.324] [jointLog] [info] iteration = 100 | max rel diff. = 17.4396
[2023-09-23 19:37:51.707] [jointLog] [info] iteration = 200 | max rel diff. = 0.324637
[2023-09-23 19:38:27.233] [jointLog] [info] iteration = 300 | max rel diff. = 6.86219
[2023-09-23 19:39:02.087] [jointLog] [info] iteration = 400 | max rel diff. = 0.0455808
[2023-09-23 19:39:37.375] [jointLog] [info] iteration = 500 | max rel diff. = 0.042171
[2023-09-23 19:40:12.301] [jointLog] [info] iteration = 600 | max rel diff. = 0.222475
[2023-09-23 19:40:47.304] [jointLog] [info] iteration = 700 | max rel diff. = 0.123478
[2023-09-23 19:41:22.513] [jointLog] [info] iteration = 800 | max rel diff. = 0.0510742
[2023-09-23 19:41:56.935] [jointLog] [info] iteration = 900 | max rel diff. = 0.0345569
[2023-09-23 19:42:15.894] [jointLog] [info] iteration = 955 | max rel diff. = 0.00564284
[2023-09-23 19:42:18.094] [jointLog] [info] Finished optimizer
[2023-09-23 19:42:18.094] [jointLog] [info] writing output