[2023-08-22 19:10:38.868] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-22 19:10:38.868] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-22 19:10:38.868] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-22 19:10:38.868] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-22 19:10:38.869] [jointLog] [info] parsing read library format
[2023-08-22 19:10:38.869] [jointLog] [info] There is 1 library.
[2023-08-22 19:10:38.869] [jointLog] [info] Loading pufferfish index
[2023-08-22 19:10:38.869] [jointLog] [info] Loading dense pufferfish index.
[2023-08-22 19:13:44.705] [jointLog] [info] done
[2023-08-22 19:13:45.091] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-22 19:15:15.556] [jointLog] [info] Number of decoys : 194
[2023-08-22 19:15:15.556] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-22 19:15:23.639] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-22 19:30:13.792] [jointLog] [info] Computed 342,331 rich equivalence classes for further processing
[2023-08-22 19:30:13.792] [jointLog] [info] Counted 18,171,038 total reads in the equivalence classes 
[2023-08-22 19:30:13.835] [jointLog] [info] Number of mappings discarded because of alignment score : 7,014,197
[2023-08-22 19:30:13.835] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,560,324
[2023-08-22 19:30:13.835] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 903,127
[2023-08-22 19:30:13.835] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 475,460
[2023-08-22 19:30:13.835] [jointLog] [info] Mapping rate = 90.9903%

[2023-08-22 19:30:13.835] [jointLog] [info] finished quantifyLibrary()
[2023-08-22 19:30:13.836] [jointLog] [info] Starting optimizer
[2023-08-22 19:30:13.795] [fileLog] [info] 
At end of round 0
==================
Observed 19970293 total fragments (19970293 in most recent round)

[2023-08-22 19:30:27.117] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-22 19:30:27.921] [jointLog] [info] iteration = 0 | max rel diff. = 234.123
[2023-08-22 19:30:35.512] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-22 19:42:55.796] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-22 19:42:55.797] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-22 19:44:18.595] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-22 19:45:25.703] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-22 19:46:46.699] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-22 19:48:01.098] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-22 19:49:18.984] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-22 19:50:38.551] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-22 19:51:53.472] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-22 19:53:09.031] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-22 19:54:30.186] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-22 19:55:37.534] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-22 19:55:37.552] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-22 19:56:58.119] [jointLog] [info] iteration = 100 | max rel diff. = 3.24098
[2023-08-22 19:58:23.072] [jointLog] [info] iteration = 200 | max rel diff. = 17.9934
[2023-08-22 19:59:47.929] [jointLog] [info] iteration = 300 | max rel diff. = 6.20477
[2023-08-22 20:01:10.125] [jointLog] [info] iteration = 400 | max rel diff. = 0.150452
[2023-08-22 20:02:30.486] [jointLog] [info] iteration = 500 | max rel diff. = 0.140186
[2023-08-22 20:04:01.560] [jointLog] [info] iteration = 600 | max rel diff. = 0.475215
[2023-08-22 20:05:23.618] [jointLog] [info] iteration = 700 | max rel diff. = 0.102378
[2023-08-22 20:06:52.986] [jointLog] [info] iteration = 800 | max rel diff. = 0.0202522
[2023-08-22 20:08:22.231] [jointLog] [info] iteration = 900 | max rel diff. = 1.34303
[2023-08-22 20:09:51.137] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0242496
[2023-08-22 20:11:18.962] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0733132
[2023-08-22 20:11:31.496] [jointLog] [info] iteration = 1,115 | max rel diff. = 0.00577346
[2023-08-22 20:11:34.637] [jointLog] [info] Finished optimizer
[2023-08-22 20:11:34.637] [jointLog] [info] writing output