[2023-09-08 04:01:27.025] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-08 04:01:27.025] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-08 04:01:27.025] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-08 04:01:27.025] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-08 04:01:27.025] [jointLog] [info] parsing read library format
[2023-09-08 04:01:27.025] [jointLog] [info] There is 1 library.
[2023-09-08 04:01:27.025] [jointLog] [info] Loading pufferfish index
[2023-09-08 04:01:27.026] [jointLog] [info] Loading dense pufferfish index.
[2023-09-08 04:02:48.415] [jointLog] [info] done
[2023-09-08 04:02:48.545] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-08 04:03:24.763] [jointLog] [info] Number of decoys : 194
[2023-09-08 04:03:24.763] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-08 04:03:27.341] [jointLog] [info] Automatically detected most likely library type as IU

[2023-09-08 04:09:35.434] [fileLog] [info] 
At end of round 0
==================
Observed 25005168 total fragments (25005168 in most recent round)

[2023-09-08 04:09:35.433] [jointLog] [info] Computed 273,043 rich equivalence classes for further processing
[2023-09-08 04:09:35.433] [jointLog] [info] Counted 23,060,910 total reads in the equivalence classes 
[2023-09-08 04:09:35.444] [jointLog] [info] Number of mappings discarded because of alignment score : 9,386,513
[2023-09-08 04:09:35.444] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,757,079
[2023-09-08 04:09:35.444] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 613,200
[2023-09-08 04:09:35.444] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 409,924
[2023-09-08 04:09:35.444] [jointLog] [info] Mapping rate = 92.2246%

[2023-09-08 04:09:35.444] [jointLog] [info] finished quantifyLibrary()
[2023-09-08 04:09:35.444] [jointLog] [info] Starting optimizer
[2023-09-08 04:09:39.747] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-08 04:09:40.098] [jointLog] [info] iteration = 0 | max rel diff. = 315.694
[2023-09-08 04:09:43.639] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-08 04:13:49.743] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-08 04:13:49.743] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-08 04:14:09.877] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-08 04:14:30.018] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-08 04:14:50.917] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-08 04:15:11.658] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-08 04:15:31.726] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-08 04:15:52.317] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-08 04:16:12.271] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-08 04:16:31.528] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-08 04:16:51.196] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-08 04:17:11.589] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-08 04:17:44.971] [jointLog] [info] iteration = 100 | max rel diff. = 5.26727
[2023-09-08 04:18:21.922] [jointLog] [info] iteration = 200 | max rel diff. = 2.71374
[2023-09-08 04:18:59.125] [jointLog] [info] iteration = 300 | max rel diff. = 0.868946
[2023-09-08 04:19:36.359] [jointLog] [info] iteration = 400 | max rel diff. = 3.95612
[2023-09-08 04:20:13.523] [jointLog] [info] iteration = 500 | max rel diff. = 0.313956
[2023-09-08 04:20:49.940] [jointLog] [info] iteration = 600 | max rel diff. = 1.28308
[2023-09-08 04:21:25.003] [jointLog] [info] iteration = 700 | max rel diff. = 0.20486
[2023-09-08 04:21:59.802] [jointLog] [info] iteration = 800 | max rel diff. = 0.0358232
[2023-09-08 04:22:18.306] [jointLog] [info] iteration = 854 | max rel diff. = 0.00961551
[2023-09-08 04:22:20.806] [jointLog] [info] Finished optimizer
[2023-09-08 04:22:20.806] [jointLog] [info] writing output