[2023-08-30 14:51:45.102] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-30 14:51:45.102] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-30 14:51:45.102] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-30 14:51:45.102] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-30 14:51:45.102] [jointLog] [info] parsing read library format
[2023-08-30 14:51:45.103] [jointLog] [info] There is 1 library.
[2023-08-30 14:51:45.103] [jointLog] [info] Loading pufferfish index
[2023-08-30 14:51:45.103] [jointLog] [info] Loading dense pufferfish index.
[2023-08-30 14:52:58.735] [jointLog] [info] done
[2023-08-30 14:52:58.888] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-30 14:53:38.382] [jointLog] [info] Number of decoys : 194
[2023-08-30 14:53:38.382] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-30 14:53:40.321] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-30 14:53:41.223] [jointLog] [info] Automatically detected most likely library type as SR

[2023-08-30 15:04:23.827] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments
[2023-08-30 15:04:23.942] [jointLog] [info] Thread saw mini-batch with a maximum of 4.50% zero probability fragments
[2023-08-30 15:04:24.043] [jointLog] [info] Thread saw mini-batch with a maximum of 4.54% zero probability fragments
[2023-08-30 15:04:24.302] [jointLog] [info] Thread saw mini-batch with a maximum of 4.58% zero probability fragments
[2023-08-30 15:04:24.353] [jointLog] [info] Thread saw mini-batch with a maximum of 4.66% zero probability fragments
[2023-08-30 15:04:24.372] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-08-30 15:04:24.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2023-08-30 15:04:24.600] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-08-30 15:04:25.226] [jointLog] [info] Computed 435,589 rich equivalence classes for further processing
[2023-08-30 15:04:25.226] [jointLog] [info] Counted 45,782,597 total reads in the equivalence classes 
[2023-08-30 15:04:25.237] [jointLog] [info] Number of mappings discarded because of alignment score : 522,527,374
[2023-08-30 15:04:25.237] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,744,019
[2023-08-30 15:04:25.237] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 633,633
[2023-08-30 15:04:25.237] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-30 15:04:25.237] [jointLog] [info] Mapping rate = 89.4564%

[2023-08-30 15:04:25.237] [jointLog] [info] finished quantifyLibrary()
[2023-08-30 15:04:25.237] [jointLog] [info] Starting optimizer
[2023-08-30 15:04:25.227] [fileLog] [info] 
At end of round 0
==================
Observed 51178672 total fragments (51178672 in most recent round)

[2023-08-30 15:04:31.814] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-30 15:04:32.219] [jointLog] [info] iteration = 0 | max rel diff. = 627.617
[2023-08-30 15:04:36.231] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-30 15:07:25.989] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-30 15:07:25.990] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-30 15:07:44.307] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-30 15:08:03.305] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-30 15:08:22.796] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-30 15:08:41.309] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-30 15:08:55.750] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-30 15:09:11.780] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-30 15:09:25.849] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-30 15:09:39.173] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-30 15:09:54.534] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-30 15:10:11.158] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 15:10:11.159] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 15:10:46.651] [jointLog] [info] iteration = 100 | max rel diff. = 19.9649
[2023-08-30 15:11:28.585] [jointLog] [info] iteration = 200 | max rel diff. = 19.0674
[2023-08-30 15:12:13.156] [jointLog] [info] iteration = 300 | max rel diff. = 1.56582
[2023-08-30 15:13:00.207] [jointLog] [info] iteration = 400 | max rel diff. = 0.446809
[2023-08-30 15:14:02.961] [jointLog] [info] iteration = 500 | max rel diff. = 0.127301
[2023-08-30 15:15:03.854] [jointLog] [info] iteration = 600 | max rel diff. = 0.170702
[2023-08-30 15:16:04.815] [jointLog] [info] iteration = 700 | max rel diff. = 1.0698
[2023-08-30 15:17:08.882] [jointLog] [info] iteration = 800 | max rel diff. = 3.15129
[2023-08-30 15:18:10.071] [jointLog] [info] iteration = 900 | max rel diff. = 0.201667
[2023-08-30 15:19:14.366] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.65082
[2023-08-30 15:20:18.385] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0830238
[2023-08-30 15:21:17.103] [jointLog] [info] iteration = 1,194 | max rel diff. = 0.00665639
[2023-08-30 15:21:19.930] [jointLog] [info] Finished optimizer
[2023-08-30 15:21:19.930] [jointLog] [info] writing output