[2023-08-21 16:52:56.668] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-21 16:52:56.668] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-21 16:52:56.668] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-21 16:52:56.668] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-21 16:52:56.668] [jointLog] [info] parsing read library format
[2023-08-21 16:52:56.668] [jointLog] [info] There is 1 library.
[2023-08-21 16:52:56.668] [jointLog] [info] Loading pufferfish index
[2023-08-21 16:52:56.669] [jointLog] [info] Loading dense pufferfish index.
[2023-08-21 16:56:03.843] [jointLog] [info] done
[2023-08-21 16:56:04.043] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-21 16:57:23.318] [jointLog] [info] Number of decoys : 194
[2023-08-21 16:57:23.318] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-21 16:57:28.329] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-21 17:18:58.679] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments
[2023-08-21 17:18:58.841] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2023-08-21 17:18:59.076] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-08-21 17:18:59.345] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-08-21 17:18:59.452] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-08-21 17:18:59.494] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-08-21 17:18:59.961] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments
[2023-08-21 17:19:00.211] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-08-21 17:19:01.191] [fileLog] [info] 
At end of round 0
==================
Observed 38269796 total fragments (38269796 in most recent round)

[2023-08-21 17:19:01.183] [jointLog] [info] Computed 279,829 rich equivalence classes for further processing
[2023-08-21 17:19:01.183] [jointLog] [info] Counted 33,949,800 total reads in the equivalence classes 
[2023-08-21 17:19:01.218] [jointLog] [info] Number of mappings discarded because of alignment score : 16,373,466
[2023-08-21 17:19:01.218] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,647,748
[2023-08-21 17:19:01.218] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,180,685
[2023-08-21 17:19:01.218] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,936,791
[2023-08-21 17:19:01.218] [jointLog] [info] Mapping rate = 88.7117%

[2023-08-21 17:19:01.218] [jointLog] [info] finished quantifyLibrary()
[2023-08-21 17:19:01.219] [jointLog] [info] Starting optimizer
[2023-08-21 17:19:11.965] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-21 17:19:12.729] [jointLog] [info] iteration = 0 | max rel diff. = 324.023
[2023-08-21 17:19:20.890] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-21 17:26:15.091] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-21 17:26:15.091] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-21 17:26:49.940] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-21 17:27:16.557] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-21 17:27:43.336] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-21 17:28:27.981] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-21 17:29:17.651] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-21 17:30:07.790] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-21 17:30:53.179] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-21 17:31:37.083] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-21 17:32:26.286] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-21 17:33:20.171] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:33:20.176] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:34:19.997] [jointLog] [info] iteration = 100 | max rel diff. = 15.2147
[2023-08-21 17:35:14.473] [jointLog] [info] iteration = 200 | max rel diff. = 4.02036
[2023-08-21 17:36:05.972] [jointLog] [info] iteration = 300 | max rel diff. = 0.292124
[2023-08-21 17:37:00.896] [jointLog] [info] iteration = 400 | max rel diff. = 0.504813
[2023-08-21 17:37:53.648] [jointLog] [info] iteration = 500 | max rel diff. = 0.263336
[2023-08-21 17:38:47.845] [jointLog] [info] iteration = 600 | max rel diff. = 0.589085
[2023-08-21 17:39:43.136] [jointLog] [info] iteration = 700 | max rel diff. = 0.350947
[2023-08-21 17:40:34.265] [jointLog] [info] iteration = 800 | max rel diff. = 0.0682487
[2023-08-21 17:41:29.826] [jointLog] [info] iteration = 900 | max rel diff. = 0.936808
[2023-08-21 17:42:31.180] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.181367
[2023-08-21 17:43:30.563] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.161591
[2023-08-21 17:44:28.662] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0699315
[2023-08-21 17:44:56.605] [jointLog] [info] iteration = 1,262 | max rel diff. = 0.0038723
[2023-08-21 17:44:58.914] [jointLog] [info] Finished optimizer
[2023-08-21 17:44:58.914] [jointLog] [info] writing output