[2023-08-25 15:12:28.214] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 15:12:28.214] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 15:12:28.214] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 15:12:28.214] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 15:12:28.214] [jointLog] [info] parsing read library format
[2023-08-25 15:12:28.215] [jointLog] [info] There is 1 library.
[2023-08-25 15:12:28.215] [jointLog] [info] Loading pufferfish index
[2023-08-25 15:12:28.215] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 15:13:41.555] [jointLog] [info] done
[2023-08-25 15:13:41.686] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 15:14:19.111] [jointLog] [info] Number of decoys : 194
[2023-08-25 15:14:19.111] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 15:14:20.149] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 15:14:21.189] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 15:20:27.571] [jointLog] [info] Thread saw mini-batch with a maximum of 4.94% zero probability fragments
[2023-08-25 15:20:27.693] [jointLog] [info] Thread saw mini-batch with a maximum of 5.08% zero probability fragments
[2023-08-25 15:20:27.729] [jointLog] [info] Thread saw mini-batch with a maximum of 4.96% zero probability fragments
[2023-08-25 15:20:27.794] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments
[2023-08-25 15:20:27.862] [jointLog] [info] Thread saw mini-batch with a maximum of 4.82% zero probability fragments
[2023-08-25 15:20:27.904] [jointLog] [info] Thread saw mini-batch with a maximum of 4.84% zero probability fragments
[2023-08-25 15:20:28.006] [jointLog] [info] Thread saw mini-batch with a maximum of 4.80% zero probability fragments
[2023-08-25 15:20:28.361] [jointLog] [info] Thread saw mini-batch with a maximum of 4.94% zero probability fragments
[2023-08-25 15:20:28.758] [jointLog] [info] Computed 359,169 rich equivalence classes for further processing
[2023-08-25 15:20:28.758] [jointLog] [info] Counted 15,652,193 total reads in the equivalence classes 
[2023-08-25 15:20:28.765] [jointLog] [info] Number of mappings discarded because of alignment score : 288,182,819
[2023-08-25 15:20:28.765] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,917,958
[2023-08-25 15:20:28.765] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 722,286
[2023-08-25 15:20:28.765] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 15:20:28.765] [jointLog] [info] Mapping rate = 77.8485%

[2023-08-25 15:20:28.765] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 15:20:28.765] [jointLog] [info] Starting optimizer
[2023-08-25 15:20:28.758] [fileLog] [info] 
At end of round 0
==================
Observed 20105969 total fragments (20105969 in most recent round)

[2023-08-25 15:20:33.098] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 15:20:33.435] [jointLog] [info] iteration = 0 | max rel diff. = 285.554
[2023-08-25 15:20:36.822] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 15:22:34.880] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 15:22:34.880] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 15:22:45.762] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 15:22:56.516] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 15:23:07.400] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 15:23:18.114] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 15:23:28.877] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 15:23:39.939] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 15:23:50.646] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 15:24:00.848] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 15:24:11.622] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 15:24:22.308] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 15:24:22.316] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 15:24:52.434] [jointLog] [info] iteration = 100 | max rel diff. = 12.0925
[2023-08-25 15:25:26.229] [jointLog] [info] iteration = 200 | max rel diff. = 16.2599
[2023-08-25 15:26:00.172] [jointLog] [info] iteration = 300 | max rel diff. = 1.03918
[2023-08-25 15:26:34.189] [jointLog] [info] iteration = 400 | max rel diff. = 0.526665
[2023-08-25 15:27:07.830] [jointLog] [info] iteration = 500 | max rel diff. = 1.62013
[2023-08-25 15:27:41.667] [jointLog] [info] iteration = 600 | max rel diff. = 0.0379389
[2023-08-25 15:28:15.098] [jointLog] [info] iteration = 700 | max rel diff. = 0.0688518
[2023-08-25 15:28:48.724] [jointLog] [info] iteration = 800 | max rel diff. = 0.311986
[2023-08-25 15:29:22.552] [jointLog] [info] iteration = 900 | max rel diff. = 0.169221
[2023-08-25 15:29:41.066] [jointLog] [info] iteration = 956 | max rel diff. = 0.0089438
[2023-08-25 15:29:42.862] [jointLog] [info] Finished optimizer
[2023-08-25 15:29:42.862] [jointLog] [info] writing output