[2023-10-03 23:39:00.772] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 23:39:00.772] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 23:39:00.772] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 23:39:00.772] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 23:39:00.772] [jointLog] [info] parsing read library format
[2023-10-03 23:39:00.772] [jointLog] [info] There is 1 library.
[2023-10-03 23:39:00.772] [jointLog] [info] Loading pufferfish index
[2023-10-03 23:39:00.772] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 23:40:14.416] [jointLog] [info] done
[2023-10-03 23:40:14.572] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 23:40:53.931] [jointLog] [info] Number of decoys : 194
[2023-10-03 23:40:53.931] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 23:40:55.940] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 23:40:56.824] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 23:41:49.780] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 23:41:49.847] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 23:41:49.883] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-03 23:41:49.952] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-10-03 23:41:49.972] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 23:41:49.998] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-10-03 23:41:50.083] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-03 23:41:50.209] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-10-03 23:41:50.373] [jointLog] [info] Computed 87,441 rich equivalence classes for further processing
[2023-10-03 23:41:50.373] [jointLog] [info] Counted 3,560,882 total reads in the equivalence classes 
[2023-10-03 23:41:50.380] [jointLog] [info] Number of mappings discarded because of alignment score : 62,183,734
[2023-10-03 23:41:50.380] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 329,253
[2023-10-03 23:41:50.380] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 96,952
[2023-10-03 23:41:50.380] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 23:41:50.374] [fileLog] [info] 
At end of round 0
==================
Observed 4644083 total fragments (4644083 in most recent round)

[2023-10-03 23:41:51.570] [jointLog] [warning] Only 3560882 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 23:41:51.570] [jointLog] [info] Mapping rate = 76.6757%

[2023-10-03 23:41:51.570] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 23:41:51.570] [jointLog] [info] Starting optimizer
[2023-10-03 23:41:56.270] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 23:41:56.608] [jointLog] [info] iteration = 0 | max rel diff. = 79.9304
[2023-10-03 23:41:59.944] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 23:42:57.597] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 23:42:57.597] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 23:43:03.069] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 23:43:08.564] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 23:43:14.087] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 23:43:19.741] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 23:43:25.303] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 23:43:30.485] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 23:43:35.791] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 23:43:41.002] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 23:43:46.787] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 23:43:52.210] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 23:44:23.267] [jointLog] [info] iteration = 100 | max rel diff. = 2.1893
[2023-10-03 23:44:57.869] [jointLog] [info] iteration = 200 | max rel diff. = 5.84119
[2023-10-03 23:45:32.250] [jointLog] [info] iteration = 300 | max rel diff. = 0.187021
[2023-10-03 23:46:07.087] [jointLog] [info] iteration = 400 | max rel diff. = 0.248137
[2023-10-03 23:46:41.958] [jointLog] [info] iteration = 500 | max rel diff. = 0.0271595
[2023-10-03 23:47:16.168] [jointLog] [info] iteration = 600 | max rel diff. = 0.0326091
[2023-10-03 23:47:50.246] [jointLog] [info] iteration = 700 | max rel diff. = 0.0399018
[2023-10-03 23:48:24.160] [jointLog] [info] iteration = 800 | max rel diff. = 0.770504
[2023-10-03 23:48:47.354] [jointLog] [info] iteration = 869 | max rel diff. = 0.00602774
[2023-10-03 23:48:49.488] [jointLog] [info] Finished optimizer
[2023-10-03 23:48:49.488] [jointLog] [info] writing output