[2023-08-27 18:13:39.294] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 18:13:39.294] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 18:13:39.294] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 18:13:39.294] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 18:13:39.294] [jointLog] [info] parsing read library format
[2023-08-27 18:13:39.294] [jointLog] [info] There is 1 library.
[2023-08-27 18:13:39.294] [jointLog] [info] Loading pufferfish index
[2023-08-27 18:13:39.294] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 18:14:51.212] [jointLog] [info] done
[2023-08-27 18:14:51.335] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 18:15:26.798] [jointLog] [info] Number of decoys : 194
[2023-08-27 18:15:26.798] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 18:15:29.174] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-27 18:21:45.164] [jointLog] [info] Computed 217,901 rich equivalence classes for further processing
[2023-08-27 18:21:45.164] [jointLog] [info] Counted 26,794,219 total reads in the equivalence classes 
[2023-08-27 18:21:45.172] [jointLog] [info] Number of mappings discarded because of alignment score : 9,287,191
[2023-08-27 18:21:45.172] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,509,906
[2023-08-27 18:21:45.172] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 796,533
[2023-08-27 18:21:45.172] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 658,320
[2023-08-27 18:21:45.172] [jointLog] [info] Mapping rate = 93.1148%

[2023-08-27 18:21:45.172] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 18:21:45.174] [jointLog] [info] Starting optimizer
[2023-08-27 18:21:45.165] [fileLog] [info] 
At end of round 0
==================
Observed 28775479 total fragments (28775479 in most recent round)

[2023-08-27 18:21:49.145] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 18:21:49.485] [jointLog] [info] iteration = 0 | max rel diff. = 317.745
[2023-08-27 18:21:52.858] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 18:24:51.230] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 18:24:51.230] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 18:25:05.925] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 18:25:20.950] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 18:25:35.284] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 18:25:50.695] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 18:26:05.374] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 18:26:19.729] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 18:26:34.501] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 18:26:49.231] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 18:27:04.387] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 18:27:18.777] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 18:27:18.780] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 18:27:47.490] [jointLog] [info] iteration = 100 | max rel diff. = 14.0917
[2023-08-27 18:28:19.653] [jointLog] [info] iteration = 200 | max rel diff. = 0.402566
[2023-08-27 18:28:52.139] [jointLog] [info] iteration = 300 | max rel diff. = 0.598573
[2023-08-27 18:29:25.247] [jointLog] [info] iteration = 400 | max rel diff. = 5.48361
[2023-08-27 18:29:58.341] [jointLog] [info] iteration = 500 | max rel diff. = 0.140607
[2023-08-27 18:30:31.423] [jointLog] [info] iteration = 600 | max rel diff. = 5.23427
[2023-08-27 18:31:04.570] [jointLog] [info] iteration = 700 | max rel diff. = 1.24192
[2023-08-27 18:31:38.293] [jointLog] [info] iteration = 800 | max rel diff. = 0.0444854
[2023-08-27 18:32:11.506] [jointLog] [info] iteration = 900 | max rel diff. = 0.0626813
[2023-08-27 18:32:37.472] [jointLog] [info] iteration = 980 | max rel diff. = 0.00665517
[2023-08-27 18:32:39.262] [jointLog] [info] Finished optimizer
[2023-08-27 18:32:39.262] [jointLog] [info] writing output