[2023-08-28 17:36:53.588] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 17:36:53.588] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 17:36:53.588] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 17:36:53.588] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 17:36:53.588] [jointLog] [info] parsing read library format
[2023-08-28 17:36:53.588] [jointLog] [info] There is 1 library.
[2023-08-28 17:36:53.588] [jointLog] [info] Loading pufferfish index
[2023-08-28 17:36:53.588] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 17:39:10.973] [jointLog] [info] done
[2023-08-28 17:39:11.238] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 17:40:10.036] [jointLog] [info] Number of decoys : 194
[2023-08-28 17:40:10.036] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 17:40:15.979] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-28 17:52:58.774] [fileLog] [info] 
At end of round 0
==================
Observed 23342904 total fragments (23342904 in most recent round)

[2023-08-28 17:52:58.773] [jointLog] [info] Computed 480,659 rich equivalence classes for further processing
[2023-08-28 17:52:58.773] [jointLog] [info] Counted 20,232,733 total reads in the equivalence classes 
[2023-08-28 17:52:58.786] [jointLog] [info] Number of mappings discarded because of alignment score : 8,400,691
[2023-08-28 17:52:58.786] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,297,576
[2023-08-28 17:52:58.786] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,336,862
[2023-08-28 17:52:58.786] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 492,583
[2023-08-28 17:52:58.786] [jointLog] [info] Mapping rate = 86.6762%

[2023-08-28 17:52:58.786] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 17:52:58.787] [jointLog] [info] Starting optimizer
[2023-08-28 17:53:04.835] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 17:53:05.401] [jointLog] [info] iteration = 0 | max rel diff. = 288.829
[2023-08-28 17:53:10.708] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 18:06:22.382] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 18:06:22.382] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 18:07:40.096] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 18:08:50.942] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 18:10:10.698] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 18:11:22.281] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 18:12:41.484] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 18:13:57.038] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 18:15:14.352] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 18:16:23.570] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 18:17:41.447] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 18:18:52.354] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 18:19:39.132] [jointLog] [info] iteration = 100 | max rel diff. = 17.5954
[2023-08-28 18:20:28.789] [jointLog] [info] iteration = 200 | max rel diff. = 0.884669
[2023-08-28 18:21:19.229] [jointLog] [info] iteration = 300 | max rel diff. = 0.134893
[2023-08-28 18:22:08.484] [jointLog] [info] iteration = 400 | max rel diff. = 0.286822
[2023-08-28 18:22:54.921] [jointLog] [info] iteration = 500 | max rel diff. = 0.47012
[2023-08-28 18:23:43.526] [jointLog] [info] iteration = 600 | max rel diff. = 0.159803
[2023-08-28 18:24:32.598] [jointLog] [info] iteration = 700 | max rel diff. = 0.076085
[2023-08-28 18:25:21.322] [jointLog] [info] iteration = 800 | max rel diff. = 0.187009
[2023-08-28 18:26:07.237] [jointLog] [info] iteration = 900 | max rel diff. = 0.0215792
[2023-08-28 18:26:56.003] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.151076
[2023-08-28 18:27:30.982] [jointLog] [info] iteration = 1,073 | max rel diff. = 0.00387606
[2023-08-28 18:27:33.231] [jointLog] [info] Finished optimizer
[2023-08-28 18:27:33.231] [jointLog] [info] writing output