[2023-10-04 00:23:30.849] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 00:23:30.849] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 00:23:30.849] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 00:23:30.849] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 00:23:30.849] [jointLog] [info] parsing read library format
[2023-10-04 00:23:30.850] [jointLog] [info] There is 1 library.
[2023-10-04 00:23:30.850] [jointLog] [info] Loading pufferfish index
[2023-10-04 00:23:30.850] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 00:24:46.973] [jointLog] [info] done
[2023-10-04 00:24:47.122] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 00:25:25.456] [jointLog] [info] Number of decoys : 194
[2023-10-04 00:25:25.456] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 00:25:27.451] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 00:25:28.019] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 00:26:16.472] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 00:26:16.510] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-04 00:26:16.641] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-04 00:26:16.719] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 00:26:16.720] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-04 00:26:16.733] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-04 00:26:16.788] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-04 00:26:16.814] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-10-04 00:26:17.013] [jointLog] [info] Computed 84,426 rich equivalence classes for further processing
[2023-10-04 00:26:17.013] [jointLog] [info] Counted 3,944,972 total reads in the equivalence classes 
[2023-10-04 00:26:17.023] [jointLog] [info] Number of mappings discarded because of alignment score : 50,610,787
[2023-10-04 00:26:17.023] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 383,492
[2023-10-04 00:26:17.023] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 113,079
[2023-10-04 00:26:17.023] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 00:26:17.014] [fileLog] [info] 
At end of round 0
==================
Observed 5129380 total fragments (5129380 in most recent round)

[2023-10-04 00:26:18.217] [jointLog] [warning] Only 3944972 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 00:26:18.217] [jointLog] [info] Mapping rate = 76.9093%

[2023-10-04 00:26:18.217] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 00:26:18.217] [jointLog] [info] Starting optimizer
[2023-10-04 00:26:23.279] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 00:26:23.610] [jointLog] [info] iteration = 0 | max rel diff. = 88.8306
[2023-10-04 00:26:26.887] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 00:27:21.909] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 00:27:21.910] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 00:27:26.577] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 00:27:31.603] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 00:27:37.027] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 00:27:42.258] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 00:27:47.240] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 00:27:52.289] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 00:27:57.670] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 00:28:02.930] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 00:28:07.862] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 00:28:12.669] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 00:28:42.111] [jointLog] [info] iteration = 100 | max rel diff. = 20.274
[2023-10-04 00:29:16.493] [jointLog] [info] iteration = 200 | max rel diff. = 0.772757
[2023-10-04 00:29:50.971] [jointLog] [info] iteration = 300 | max rel diff. = 0.441901
[2023-10-04 00:30:25.389] [jointLog] [info] iteration = 400 | max rel diff. = 0.588048
[2023-10-04 00:30:59.704] [jointLog] [info] iteration = 500 | max rel diff. = 0.124935
[2023-10-04 00:31:35.623] [jointLog] [info] iteration = 600 | max rel diff. = 0.0709817
[2023-10-04 00:32:12.571] [jointLog] [info] iteration = 700 | max rel diff. = 0.454482
[2023-10-04 00:32:45.552] [jointLog] [info] iteration = 786 | max rel diff. = 0.00549122
[2023-10-04 00:32:48.213] [jointLog] [info] Finished optimizer
[2023-10-04 00:32:48.213] [jointLog] [info] writing output