[2023-08-28 06:16:19.285] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 06:16:19.285] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 06:16:19.285] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 06:16:19.285] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 06:16:19.285] [jointLog] [info] parsing read library format
[2023-08-28 06:16:19.285] [jointLog] [info] There is 1 library.
[2023-08-28 06:16:19.285] [jointLog] [info] Loading pufferfish index
[2023-08-28 06:16:19.285] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 06:17:39.258] [jointLog] [info] done
[2023-08-28 06:17:39.434] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 06:18:19.804] [jointLog] [info] Number of decoys : 194
[2023-08-28 06:18:19.804] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 06:18:22.530] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-28 06:18:23.994] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-28 06:23:46.761] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-08-28 06:23:46.806] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-08-28 06:23:46.817] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-08-28 06:23:46.828] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-08-28 06:23:46.886] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-08-28 06:23:47.089] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-08-28 06:23:47.194] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-08-28 06:23:47.282] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-08-28 06:23:47.638] [jointLog] [info] Computed 207,560 rich equivalence classes for further processing
[2023-08-28 06:23:47.638] [jointLog] [info] Counted 7,893,133 total reads in the equivalence classes 
[2023-08-28 06:23:47.646] [jointLog] [info] Number of mappings discarded because of alignment score : 419,517,934
[2023-08-28 06:23:47.646] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,730,912
[2023-08-28 06:23:47.646] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 379,892
[2023-08-28 06:23:47.646] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-28 06:23:47.646] [jointLog] [info] Mapping rate = 48.4938%

[2023-08-28 06:23:47.646] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 06:23:47.647] [jointLog] [info] Starting optimizer
[2023-08-28 06:23:47.640] [fileLog] [info] 
At end of round 0
==================
Observed 16276576 total fragments (16276576 in most recent round)

[2023-08-28 06:23:53.423] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 06:23:53.762] [jointLog] [info] iteration = 0 | max rel diff. = 135.089
[2023-08-28 06:23:57.173] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 06:25:17.497] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 06:25:17.498] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 06:25:24.685] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 06:25:31.947] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 06:25:39.483] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 06:25:46.933] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 06:25:54.090] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 06:26:01.884] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 06:26:09.160] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 06:26:16.476] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 06:26:23.861] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 06:26:30.800] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 06:27:03.777] [jointLog] [info] iteration = 100 | max rel diff. = 2.30214
[2023-08-28 06:27:41.354] [jointLog] [info] iteration = 200 | max rel diff. = 0.803939
[2023-08-28 06:28:16.534] [jointLog] [info] iteration = 300 | max rel diff. = 1.21404
[2023-08-28 06:28:51.282] [jointLog] [info] iteration = 400 | max rel diff. = 1.93565
[2023-08-28 06:29:24.408] [jointLog] [info] iteration = 500 | max rel diff. = 0.0637908
[2023-08-28 06:29:57.510] [jointLog] [info] iteration = 600 | max rel diff. = 0.0206566
[2023-08-28 06:30:31.548] [jointLog] [info] iteration = 700 | max rel diff. = 0.0245561
[2023-08-28 06:31:04.469] [jointLog] [info] iteration = 800 | max rel diff. = 0.200507
[2023-08-28 06:31:36.522] [jointLog] [info] iteration = 898 | max rel diff. = 0.00351547
[2023-08-28 06:31:38.855] [jointLog] [info] Finished optimizer
[2023-08-28 06:31:38.855] [jointLog] [info] writing output