[2023-08-25 15:10:44.261] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 15:10:44.261] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 15:10:44.261] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 15:10:44.261] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 15:10:44.261] [jointLog] [info] parsing read library format
[2023-08-25 15:10:44.261] [jointLog] [info] There is 1 library.
[2023-08-25 15:10:44.262] [jointLog] [info] Loading pufferfish index
[2023-08-25 15:10:44.262] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 15:11:58.653] [jointLog] [info] done
[2023-08-25 15:11:58.782] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 15:12:34.454] [jointLog] [info] Number of decoys : 194
[2023-08-25 15:12:34.454] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 15:12:36.924] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-25 15:25:19.001] [fileLog] [info] 
At end of round 0
==================
Observed 62335976 total fragments (62335976 in most recent round)

[2023-08-25 15:25:19.000] [jointLog] [info] Computed 470,150 rich equivalence classes for further processing
[2023-08-25 15:25:19.000] [jointLog] [info] Counted 57,213,489 total reads in the equivalence classes 
[2023-08-25 15:25:19.007] [jointLog] [info] Number of mappings discarded because of alignment score : 25,940,115
[2023-08-25 15:25:19.007] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,540,073
[2023-08-25 15:25:19.007] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,765,793
[2023-08-25 15:25:19.007] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,146,789
[2023-08-25 15:25:19.007] [jointLog] [info] Mapping rate = 91.7825%

[2023-08-25 15:25:19.007] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 15:25:19.008] [jointLog] [info] Starting optimizer
[2023-08-25 15:25:22.860] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 15:25:23.201] [jointLog] [info] iteration = 0 | max rel diff. = 74.3117
[2023-08-25 15:25:26.631] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 15:31:50.672] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 15:31:50.672] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 15:32:22.364] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 15:32:53.760] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 15:33:24.899] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 15:33:56.543] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 15:34:27.613] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 15:34:58.908] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 15:35:30.106] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 15:36:01.371] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 15:36:33.113] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 15:37:02.996] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 15:37:33.439] [jointLog] [info] iteration = 100 | max rel diff. = 4.68915
[2023-08-25 15:38:07.334] [jointLog] [info] iteration = 200 | max rel diff. = 10.8647
[2023-08-25 15:38:41.062] [jointLog] [info] iteration = 300 | max rel diff. = 1.2734
[2023-08-25 15:39:15.010] [jointLog] [info] iteration = 400 | max rel diff. = 1.8682
[2023-08-25 15:39:48.997] [jointLog] [info] iteration = 500 | max rel diff. = 1.8857
[2023-08-25 15:40:22.243] [jointLog] [info] iteration = 600 | max rel diff. = 9.60266
[2023-08-25 15:40:55.607] [jointLog] [info] iteration = 700 | max rel diff. = 0.447172
[2023-08-25 15:41:29.104] [jointLog] [info] iteration = 800 | max rel diff. = 1.24476
[2023-08-25 15:42:02.767] [jointLog] [info] iteration = 900 | max rel diff. = 0.154619
[2023-08-25 15:42:36.307] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.160868
[2023-08-25 15:43:09.819] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0362524
[2023-08-25 15:43:44.305] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0427484
[2023-08-25 15:44:18.336] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.549061
[2023-08-25 15:44:51.855] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0389239
[2023-08-25 15:45:25.687] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0194336
[2023-08-25 15:45:47.549] [jointLog] [info] iteration = 1,566 | max rel diff. = 0.00561395
[2023-08-25 15:45:49.373] [jointLog] [info] Finished optimizer
[2023-08-25 15:45:49.373] [jointLog] [info] writing output