[2023-09-21 06:46:00.660] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 06:46:00.660] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 06:46:00.660] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 06:46:00.660] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 06:46:00.660] [jointLog] [info] parsing read library format
[2023-09-21 06:46:00.660] [jointLog] [info] There is 1 library.
[2023-09-21 06:46:00.660] [jointLog] [info] Loading pufferfish index
[2023-09-21 06:46:00.660] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 06:47:13.602] [jointLog] [info] done
[2023-09-21 06:47:13.782] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 06:47:55.414] [jointLog] [info] Number of decoys : 194
[2023-09-21 06:47:55.414] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 06:47:58.172] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 06:47:59.281] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 06:48:50.814] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-21 06:48:50.850] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-09-21 06:48:50.979] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-21 06:48:51.000] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-09-21 06:48:51.130] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-09-21 06:48:51.180] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-21 06:48:51.191] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-21 06:48:51.341] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-21 06:48:51.636] [fileLog] [info] 
At end of round 0
==================
Observed 3346591 total fragments (3346591 in most recent round)

[2023-09-21 06:48:51.635] [jointLog] [info] Computed 89,339 rich equivalence classes for further processing
[2023-09-21 06:48:51.635] [jointLog] [info] Counted 2,458,104 total reads in the equivalence classes 
[2023-09-21 06:48:51.644] [jointLog] [info] Number of mappings discarded because of alignment score : 73,919,886
[2023-09-21 06:48:51.644] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 344,153
[2023-09-21 06:48:51.644] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 79,791
[2023-09-21 06:48:51.644] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 06:48:53.796] [jointLog] [warning] Only 2458104 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 06:48:53.796] [jointLog] [info] Mapping rate = 73.451%

[2023-09-21 06:48:53.796] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 06:48:53.797] [jointLog] [info] Starting optimizer
[2023-09-21 06:48:59.758] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 06:49:00.125] [jointLog] [info] iteration = 0 | max rel diff. = 48.3381
[2023-09-21 06:49:03.715] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 06:49:54.820] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 06:49:54.820] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 06:49:59.487] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 06:50:04.073] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 06:50:08.909] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 06:50:13.849] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 06:50:18.807] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 06:50:23.761] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 06:50:28.457] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 06:50:33.111] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 06:50:37.855] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 06:50:43.176] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 06:51:15.734] [jointLog] [info] iteration = 100 | max rel diff. = 2.80519
[2023-09-21 06:51:51.293] [jointLog] [info] iteration = 200 | max rel diff. = 0.454331
[2023-09-21 06:52:26.936] [jointLog] [info] iteration = 300 | max rel diff. = 0.931459
[2023-09-21 06:53:02.210] [jointLog] [info] iteration = 400 | max rel diff. = 0.57789
[2023-09-21 06:53:37.276] [jointLog] [info] iteration = 500 | max rel diff. = 0.014589
[2023-09-21 06:54:12.184] [jointLog] [info] iteration = 600 | max rel diff. = 0.0888098
[2023-09-21 06:54:47.100] [jointLog] [info] iteration = 700 | max rel diff. = 0.114097
[2023-09-21 06:55:10.988] [jointLog] [info] iteration = 770 | max rel diff. = 0.00747561
[2023-09-21 06:55:13.543] [jointLog] [info] Finished optimizer
[2023-09-21 06:55:13.543] [jointLog] [info] writing output