[2023-08-31 15:46:20.153] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-31 15:46:20.153] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-31 15:46:20.153] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-31 15:46:20.153] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-31 15:46:20.153] [jointLog] [info] parsing read library format
[2023-08-31 15:46:20.153] [jointLog] [info] There is 1 library.
[2023-08-31 15:46:20.562] [jointLog] [info] Loading pufferfish index
[2023-08-31 15:46:20.562] [jointLog] [info] Loading dense pufferfish index.
[2023-08-31 15:48:54.840] [jointLog] [info] done
[2023-08-31 15:48:55.105] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-31 15:49:59.764] [jointLog] [info] Number of decoys : 194
[2023-08-31 15:49:59.764] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-31 15:50:04.876] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-31 16:01:47.346] [jointLog] [info] Computed 288,027 rich equivalence classes for further processing
[2023-08-31 16:01:47.346] [jointLog] [info] Counted 23,177,416 total reads in the equivalence classes 
[2023-08-31 16:01:47.359] [jointLog] [info] Number of mappings discarded because of alignment score : 10,630,390
[2023-08-31 16:01:47.359] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,686,537
[2023-08-31 16:01:47.359] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 763,915
[2023-08-31 16:01:47.359] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,452,212
[2023-08-31 16:01:47.359] [jointLog] [info] Mapping rate = 92.1279%

[2023-08-31 16:01:47.359] [jointLog] [info] finished quantifyLibrary()
[2023-08-31 16:01:47.360] [jointLog] [info] Starting optimizer
[2023-08-31 16:01:47.347] [fileLog] [info] 
At end of round 0
==================
Observed 25157862 total fragments (25157862 in most recent round)

[2023-08-31 16:01:54.355] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-31 16:01:54.906] [jointLog] [info] iteration = 0 | max rel diff. = 301.939
[2023-08-31 16:02:00.527] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-31 16:07:56.690] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-31 16:07:56.691] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-31 16:08:31.963] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-31 16:09:14.852] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-31 16:09:58.453] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-31 16:10:39.781] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-31 16:11:21.246] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-31 16:11:54.199] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-31 16:12:28.959] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-31 16:13:00.166] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-31 16:13:33.967] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-31 16:14:06.368] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-31 16:14:57.795] [jointLog] [info] iteration = 100 | max rel diff. = 19.0826
[2023-08-31 16:15:43.599] [jointLog] [info] iteration = 200 | max rel diff. = 6.21818
[2023-08-31 16:16:27.307] [jointLog] [info] iteration = 300 | max rel diff. = 0.316057
[2023-08-31 16:17:13.623] [jointLog] [info] iteration = 400 | max rel diff. = 0.315981
[2023-08-31 16:17:59.906] [jointLog] [info] iteration = 500 | max rel diff. = 2.03929
[2023-08-31 16:18:51.143] [jointLog] [info] iteration = 600 | max rel diff. = 0.152323
[2023-08-31 16:19:45.650] [jointLog] [info] iteration = 700 | max rel diff. = 7.99529
[2023-08-31 16:20:36.674] [jointLog] [info] iteration = 800 | max rel diff. = 0.0317597
[2023-08-31 16:21:29.280] [jointLog] [info] iteration = 900 | max rel diff. = 0.177044
[2023-08-31 16:22:17.595] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.261603
[2023-08-31 16:23:02.052] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.878084
[2023-08-31 16:23:58.399] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0250073
[2023-08-31 16:24:29.476] [jointLog] [info] iteration = 1,269 | max rel diff. = 0.00985447
[2023-08-31 16:24:32.050] [jointLog] [info] Finished optimizer
[2023-08-31 16:24:32.050] [jointLog] [info] writing output