[2023-08-27 16:31:22.554] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 16:31:22.554] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 16:31:22.554] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 16:31:22.554] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 16:31:22.554] [jointLog] [info] parsing read library format
[2023-08-27 16:31:22.554] [jointLog] [info] There is 1 library.
[2023-08-27 16:31:22.555] [jointLog] [info] Loading pufferfish index
[2023-08-27 16:31:22.555] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 16:32:40.388] [jointLog] [info] done
[2023-08-27 16:32:40.510] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 16:33:17.487] [jointLog] [info] Number of decoys : 194
[2023-08-27 16:33:17.487] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 16:33:19.115] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-27 16:33:20.855] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-27 16:39:37.732] [jointLog] [info] Thread saw mini-batch with a maximum of 8.58% zero probability fragments
[2023-08-27 16:39:37.733] [jointLog] [info] Thread saw mini-batch with a maximum of 8.84% zero probability fragments
[2023-08-27 16:39:37.841] [jointLog] [info] Thread saw mini-batch with a maximum of 9.30% zero probability fragments
[2023-08-27 16:39:38.017] [jointLog] [info] Thread saw mini-batch with a maximum of 9.62% zero probability fragments
[2023-08-27 16:39:38.148] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments
[2023-08-27 16:39:38.198] [jointLog] [info] Thread saw mini-batch with a maximum of 9.50% zero probability fragments
[2023-08-27 16:39:38.271] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2023-08-27 16:39:38.677] [jointLog] [info] Thread saw mini-batch with a maximum of 9.48% zero probability fragments
[2023-08-27 16:39:39.084] [jointLog] [info] Computed 350,382 rich equivalence classes for further processing
[2023-08-27 16:39:39.084] [jointLog] [info] Counted 6,724,157 total reads in the equivalence classes 
[2023-08-27 16:39:39.091] [jointLog] [info] Number of mappings discarded because of alignment score : 480,719,261
[2023-08-27 16:39:39.091] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,398,053
[2023-08-27 16:39:39.091] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 319,577
[2023-08-27 16:39:39.091] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-27 16:39:39.091] [jointLog] [info] Mapping rate = 47.7212%

[2023-08-27 16:39:39.091] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 16:39:39.091] [jointLog] [info] Starting optimizer
[2023-08-27 16:39:39.085] [fileLog] [info] 
At end of round 0
==================
Observed 14090517 total fragments (14090517 in most recent round)

[2023-08-27 16:39:43.757] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 16:39:44.099] [jointLog] [info] iteration = 0 | max rel diff. = 143.449
[2023-08-27 16:39:47.619] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 16:41:41.122] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 16:41:41.122] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 16:41:51.564] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 16:42:02.204] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 16:42:12.166] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 16:42:22.701] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 16:42:32.678] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 16:42:45.376] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 16:42:56.163] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 16:43:06.574] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 16:43:17.061] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 16:43:26.399] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:43:26.400] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:43:56.795] [jointLog] [info] iteration = 100 | max rel diff. = 14.3434
[2023-08-27 16:44:31.363] [jointLog] [info] iteration = 200 | max rel diff. = 13.4892
[2023-08-27 16:45:05.310] [jointLog] [info] iteration = 300 | max rel diff. = 1.85121
[2023-08-27 16:45:39.130] [jointLog] [info] iteration = 400 | max rel diff. = 0.212209
[2023-08-27 16:46:12.879] [jointLog] [info] iteration = 500 | max rel diff. = 0.428447
[2023-08-27 16:46:46.464] [jointLog] [info] iteration = 600 | max rel diff. = 0.0257273
[2023-08-27 16:47:19.982] [jointLog] [info] iteration = 700 | max rel diff. = 0.527436
[2023-08-27 16:47:53.756] [jointLog] [info] iteration = 800 | max rel diff. = 0.0856033
[2023-08-27 16:48:27.408] [jointLog] [info] iteration = 900 | max rel diff. = 0.0967665
[2023-08-27 16:49:01.025] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0128182
[2023-08-27 16:49:22.603] [jointLog] [info] iteration = 1,067 | max rel diff. = 0.00877902
[2023-08-27 16:49:24.301] [jointLog] [info] Finished optimizer
[2023-08-27 16:49:24.301] [jointLog] [info] writing output