[2023-09-15 19:16:07.576] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-15 19:16:07.576] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-15 19:16:07.576] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-15 19:16:07.576] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-15 19:16:07.576] [jointLog] [info] parsing read library format
[2023-09-15 19:16:07.576] [jointLog] [info] There is 1 library.
[2023-09-15 19:16:07.576] [jointLog] [info] Loading pufferfish index
[2023-09-15 19:16:07.577] [jointLog] [info] Loading dense pufferfish index.
[2023-09-15 19:17:24.705] [jointLog] [info] done
[2023-09-15 19:17:24.863] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-15 19:18:05.062] [jointLog] [info] Number of decoys : 194
[2023-09-15 19:18:05.062] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-15 19:18:07.591] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-15 19:18:08.315] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-15 19:18:41.762] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-09-15 19:18:41.810] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-09-15 19:18:41.895] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-09-15 19:18:41.941] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-15 19:18:41.944] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-09-15 19:18:41.991] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-09-15 19:18:42.004] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-09-15 19:18:42.025] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-09-15 19:18:42.291] [fileLog] [info] 
At end of round 0
==================
Observed 5494159 total fragments (5494159 in most recent round)

[2023-09-15 19:18:42.290] [jointLog] [info] Computed 153,499 rich equivalence classes for further processing
[2023-09-15 19:18:42.290] [jointLog] [info] Counted 4,252,911 total reads in the equivalence classes 
[2023-09-15 19:18:42.299] [jointLog] [info] Number of mappings discarded because of alignment score : 7,934,207
[2023-09-15 19:18:42.299] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 122,314
[2023-09-15 19:18:42.299] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 42,825
[2023-09-15 19:18:42.299] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-15 19:18:43.882] [jointLog] [warning] Only 4252911 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-15 19:18:43.882] [jointLog] [info] Mapping rate = 77.4079%

[2023-09-15 19:18:43.882] [jointLog] [info] finished quantifyLibrary()
[2023-09-15 19:18:43.883] [jointLog] [info] Starting optimizer
[2023-09-15 19:18:49.035] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-15 19:18:49.421] [jointLog] [info] iteration = 0 | max rel diff. = 78.4997
[2023-09-15 19:18:52.956] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-15 19:20:04.636] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-15 19:20:04.637] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-15 19:20:11.027] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-15 19:20:17.774] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-15 19:20:24.339] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-15 19:20:31.087] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-15 19:20:37.724] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-15 19:20:44.659] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-15 19:20:51.000] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-15 19:20:57.217] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-15 19:21:04.063] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-15 19:21:10.584] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-15 19:21:42.712] [jointLog] [info] iteration = 100 | max rel diff. = 14.3698
[2023-09-15 19:22:17.707] [jointLog] [info] iteration = 200 | max rel diff. = 1.00354
[2023-09-15 19:22:51.977] [jointLog] [info] iteration = 300 | max rel diff. = 1.32767
[2023-09-15 19:23:25.648] [jointLog] [info] iteration = 400 | max rel diff. = 6.31337
[2023-09-15 19:24:01.003] [jointLog] [info] iteration = 500 | max rel diff. = 1.07279
[2023-09-15 19:24:36.758] [jointLog] [info] iteration = 600 | max rel diff. = 0.180121
[2023-09-15 19:25:12.604] [jointLog] [info] iteration = 700 | max rel diff. = 0.0975488
[2023-09-15 19:25:48.172] [jointLog] [info] iteration = 800 | max rel diff. = 0.119698
[2023-09-15 19:26:23.597] [jointLog] [info] iteration = 900 | max rel diff. = 0.455712
[2023-09-15 19:26:58.456] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.108763
[2023-09-15 19:27:10.349] [jointLog] [info] iteration = 1,035 | max rel diff. = 0.00561507
[2023-09-15 19:27:12.706] [jointLog] [info] Finished optimizer
[2023-09-15 19:27:12.706] [jointLog] [info] writing output