[2023-08-31 18:11:24.341] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-31 18:11:24.341] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-31 18:11:24.341] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-31 18:11:24.341] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-31 18:11:24.341] [jointLog] [info] parsing read library format
[2023-08-31 18:11:24.341] [jointLog] [info] There is 1 library.
[2023-08-31 18:11:24.341] [jointLog] [info] Loading pufferfish index
[2023-08-31 18:11:24.342] [jointLog] [info] Loading dense pufferfish index.
[2023-08-31 18:13:09.984] [jointLog] [info] done
[2023-08-31 18:13:10.139] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-31 18:14:01.279] [jointLog] [info] Number of decoys : 194
[2023-08-31 18:14:01.279] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-31 18:14:04.394] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-31 18:17:06.667] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments
[2023-08-31 18:17:06.754] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments
[2023-08-31 18:17:06.795] [jointLog] [info] Thread saw mini-batch with a maximum of 4.48% zero probability fragments
[2023-08-31 18:17:06.863] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2023-08-31 18:17:06.864] [jointLog] [info] Thread saw mini-batch with a maximum of 4.54% zero probability fragments
[2023-08-31 18:17:06.902] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-08-31 18:17:07.046] [jointLog] [info] Thread saw mini-batch with a maximum of 4.58% zero probability fragments
[2023-08-31 18:17:07.109] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-08-31 18:17:07.628] [jointLog] [info] Computed 267,076 rich equivalence classes for further processing
[2023-08-31 18:17:07.628] [jointLog] [info] Counted 13,482,733 total reads in the equivalence classes 
[2023-08-31 18:17:07.636] [jointLog] [info] Number of mappings discarded because of alignment score : 6,745,940
[2023-08-31 18:17:07.636] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 536,705
[2023-08-31 18:17:07.636] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 332,222
[2023-08-31 18:17:07.636] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 68,531
[2023-08-31 18:17:07.636] [jointLog] [info] Mapping rate = 91.0518%

[2023-08-31 18:17:07.637] [jointLog] [info] finished quantifyLibrary()
[2023-08-31 18:17:07.637] [jointLog] [info] Starting optimizer
[2023-08-31 18:17:07.629] [fileLog] [info] 
At end of round 0
==================
Observed 14807761 total fragments (14807761 in most recent round)

[2023-08-31 18:17:11.939] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-31 18:17:12.309] [jointLog] [info] iteration = 0 | max rel diff. = 214.231
[2023-08-31 18:17:16.202] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-31 18:23:42.533] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-31 18:23:42.533] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-31 18:24:22.134] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-31 18:25:05.349] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-31 18:25:50.906] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-31 18:26:34.610] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-31 18:27:17.287] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-31 18:28:01.460] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-31 18:28:49.096] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-31 18:29:34.234] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-31 18:30:19.171] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-31 18:31:01.149] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-31 18:31:38.429] [jointLog] [info] iteration = 100 | max rel diff. = 17.1182
[2023-08-31 18:32:20.307] [jointLog] [info] iteration = 200 | max rel diff. = 1.46048
[2023-08-31 18:33:01.402] [jointLog] [info] iteration = 300 | max rel diff. = 0.362174
[2023-08-31 18:33:41.744] [jointLog] [info] iteration = 400 | max rel diff. = 7.25868
[2023-08-31 18:34:25.561] [jointLog] [info] iteration = 500 | max rel diff. = 0.201686
[2023-08-31 18:35:09.564] [jointLog] [info] iteration = 600 | max rel diff. = 0.112623
[2023-08-31 18:35:52.798] [jointLog] [info] iteration = 700 | max rel diff. = 0.104551
[2023-08-31 18:36:38.419] [jointLog] [info] iteration = 800 | max rel diff. = 0.271626
[2023-08-31 18:37:22.048] [jointLog] [info] iteration = 900 | max rel diff. = 0.108558
[2023-08-31 18:38:07.706] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0858649
[2023-08-31 18:38:54.317] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.03431
[2023-08-31 18:39:38.205] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0116816
[2023-08-31 18:40:24.452] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0376377
[2023-08-31 18:41:09.721] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0255514
[2023-08-31 18:41:52.854] [jointLog] [info] iteration = 1,500 | max rel diff. = 4.63692
[2023-08-31 18:41:53.270] [jointLog] [info] iteration = 1,502 | max rel diff. = 0.00627191
[2023-08-31 18:41:55.134] [jointLog] [info] Finished optimizer
[2023-08-31 18:41:55.134] [jointLog] [info] writing output