[2023-08-27 16:32:32.044] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 16:32:32.044] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 16:32:32.044] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 16:32:32.044] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 16:32:32.044] [jointLog] [info] parsing read library format
[2023-08-27 16:32:32.044] [jointLog] [info] There is 1 library.
[2023-08-27 16:32:32.044] [jointLog] [info] Loading pufferfish index
[2023-08-27 16:32:32.044] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 16:33:49.195] [jointLog] [info] done
[2023-08-27 16:33:49.359] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 16:34:29.559] [jointLog] [info] Number of decoys : 194
[2023-08-27 16:34:29.559] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 16:34:32.495] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-27 16:42:17.830] [jointLog] [info] Computed 240,157 rich equivalence classes for further processing
[2023-08-27 16:42:17.830] [jointLog] [info] Counted 29,406,988 total reads in the equivalence classes 
[2023-08-27 16:42:17.842] [jointLog] [info] Number of mappings discarded because of alignment score : 10,439,639
[2023-08-27 16:42:17.842] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,737,512
[2023-08-27 16:42:17.842] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 889,529
[2023-08-27 16:42:17.842] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 694,323
[2023-08-27 16:42:17.842] [jointLog] [info] Mapping rate = 93.0699%

[2023-08-27 16:42:17.842] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 16:42:17.843] [jointLog] [info] Starting optimizer
[2023-08-27 16:42:17.831] [fileLog] [info] 
At end of round 0
==================
Observed 31596672 total fragments (31596672 in most recent round)

[2023-08-27 16:42:22.962] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 16:42:23.323] [jointLog] [info] iteration = 0 | max rel diff. = 352.461
[2023-08-27 16:42:26.812] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 16:45:46.132] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 16:45:46.132] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 16:46:02.510] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 16:46:19.070] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 16:46:35.264] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 16:46:51.626] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 16:47:08.354] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 16:47:25.204] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 16:47:41.077] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 16:47:56.942] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 16:48:13.119] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 16:48:30.053] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:48:30.063] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:49:02.035] [jointLog] [info] iteration = 100 | max rel diff. = 14.4996
[2023-08-27 16:49:37.128] [jointLog] [info] iteration = 200 | max rel diff. = 15.1938
[2023-08-27 16:50:12.109] [jointLog] [info] iteration = 300 | max rel diff. = 8.30385
[2023-08-27 16:50:46.282] [jointLog] [info] iteration = 400 | max rel diff. = 10.3482
[2023-08-27 16:51:18.008] [jointLog] [info] iteration = 500 | max rel diff. = 0.136904
[2023-08-27 16:51:52.159] [jointLog] [info] iteration = 600 | max rel diff. = 0.0552504
[2023-08-27 16:52:26.866] [jointLog] [info] iteration = 700 | max rel diff. = 0.0138024
[2023-08-27 16:53:00.836] [jointLog] [info] iteration = 800 | max rel diff. = 2.19277
[2023-08-27 16:53:35.129] [jointLog] [info] iteration = 900 | max rel diff. = 0.019429
[2023-08-27 16:53:52.272] [jointLog] [info] iteration = 951 | max rel diff. = 0.00726545
[2023-08-27 16:53:54.499] [jointLog] [info] Finished optimizer
[2023-08-27 16:53:54.499] [jointLog] [info] writing output