[2023-10-03 13:22:20.535] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 13:22:20.535] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 13:22:20.535] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 13:22:20.535] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 13:22:20.535] [jointLog] [info] parsing read library format
[2023-10-03 13:22:20.536] [jointLog] [info] There is 1 library.
[2023-10-03 13:22:20.536] [jointLog] [info] Loading pufferfish index
[2023-10-03 13:22:20.536] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 13:23:41.693] [jointLog] [info] done
[2023-10-03 13:23:41.860] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 13:24:22.604] [jointLog] [info] Number of decoys : 194
[2023-10-03 13:24:22.604] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 13:24:24.612] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 13:24:25.779] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 13:25:30.358] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-03 13:25:30.477] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 13:25:30.534] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-03 13:25:30.609] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 13:25:30.714] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 13:25:30.727] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 13:25:30.755] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-03 13:25:30.881] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 13:25:31.095] [jointLog] [info] Computed 96,188 rich equivalence classes for further processing
[2023-10-03 13:25:31.095] [jointLog] [info] Counted 3,207,788 total reads in the equivalence classes 
[2023-10-03 13:25:31.118] [jointLog] [info] Number of mappings discarded because of alignment score : 68,246,318
[2023-10-03 13:25:31.118] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 454,559
[2023-10-03 13:25:31.118] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 115,058
[2023-10-03 13:25:31.118] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 13:25:31.096] [fileLog] [info] 
At end of round 0
==================
Observed 4652690 total fragments (4652690 in most recent round)

[2023-10-03 13:25:32.600] [jointLog] [warning] Only 3207788 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 13:25:32.600] [jointLog] [info] Mapping rate = 68.9448%

[2023-10-03 13:25:32.600] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 13:25:32.600] [jointLog] [info] Starting optimizer
[2023-10-03 13:25:37.380] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 13:25:37.723] [jointLog] [info] iteration = 0 | max rel diff. = 67.3998
[2023-10-03 13:25:41.211] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 13:26:48.709] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 13:26:48.710] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 13:26:54.835] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 13:27:00.785] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 13:27:06.655] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 13:27:13.109] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 13:27:19.341] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 13:27:25.520] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 13:27:31.583] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 13:27:37.511] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 13:27:43.462] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 13:27:49.466] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 13:28:18.901] [jointLog] [info] iteration = 100 | max rel diff. = 11.3974
[2023-10-03 13:28:51.412] [jointLog] [info] iteration = 200 | max rel diff. = 15.8058
[2023-10-03 13:29:23.750] [jointLog] [info] iteration = 300 | max rel diff. = 0.393653
[2023-10-03 13:29:56.220] [jointLog] [info] iteration = 400 | max rel diff. = 6.30689
[2023-10-03 13:30:29.465] [jointLog] [info] iteration = 500 | max rel diff. = 0.180912
[2023-10-03 13:31:04.653] [jointLog] [info] iteration = 600 | max rel diff. = 2.32471
[2023-10-03 13:31:39.982] [jointLog] [info] iteration = 700 | max rel diff. = 0.0186235
[2023-10-03 13:32:14.970] [jointLog] [info] iteration = 800 | max rel diff. = 1.40451
[2023-10-03 13:32:41.381] [jointLog] [info] iteration = 876 | max rel diff. = 0.00655039
[2023-10-03 13:32:43.661] [jointLog] [info] Finished optimizer
[2023-10-03 13:32:43.661] [jointLog] [info] writing output