[2023-08-21 17:10:21.142] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-21 17:10:21.142] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-21 17:10:21.142] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-21 17:10:21.142] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-21 17:10:21.142] [jointLog] [info] parsing read library format
[2023-08-21 17:10:21.142] [jointLog] [info] There is 1 library.
[2023-08-21 17:10:21.143] [jointLog] [info] Loading pufferfish index
[2023-08-21 17:10:21.143] [jointLog] [info] Loading dense pufferfish index.
[2023-08-21 17:13:13.069] [jointLog] [info] done
[2023-08-21 17:13:13.383] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-21 17:14:41.309] [jointLog] [info] Number of decoys : 194
[2023-08-21 17:14:41.309] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-21 17:14:49.053] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-21 17:25:13.338] [fileLog] [info] 
At end of round 0
==================
Observed 22413714 total fragments (22413714 in most recent round)

[2023-08-21 17:25:13.337] [jointLog] [info] Computed 367,739 rich equivalence classes for further processing
[2023-08-21 17:25:13.338] [jointLog] [info] Counted 20,660,919 total reads in the equivalence classes 
[2023-08-21 17:25:13.351] [jointLog] [info] Number of mappings discarded because of alignment score : 5,882,885
[2023-08-21 17:25:13.351] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,492,419
[2023-08-21 17:25:13.351] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 993,188
[2023-08-21 17:25:13.351] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 781,998
[2023-08-21 17:25:13.351] [jointLog] [info] Mapping rate = 92.1798%

[2023-08-21 17:25:13.351] [jointLog] [info] finished quantifyLibrary()
[2023-08-21 17:25:13.353] [jointLog] [info] Starting optimizer
[2023-08-21 17:25:36.920] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-21 17:25:37.343] [jointLog] [info] iteration = 0 | max rel diff. = 266.213
[2023-08-21 17:25:41.694] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-21 17:37:01.501] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-21 17:37:01.502] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-21 17:38:06.803] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-21 17:39:13.122] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-21 17:40:14.268] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-21 17:41:25.191] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-21 17:42:37.011] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-21 17:43:47.550] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-21 17:44:55.625] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-21 17:45:56.435] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-21 17:46:59.020] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-21 17:48:01.551] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:48:01.555] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:48:41.137] [jointLog] [info] iteration = 100 | max rel diff. = 12.686
[2023-08-21 17:49:32.701] [jointLog] [info] iteration = 200 | max rel diff. = 5.81418
[2023-08-21 17:50:30.397] [jointLog] [info] iteration = 300 | max rel diff. = 11.3704
[2023-08-21 17:51:33.016] [jointLog] [info] iteration = 400 | max rel diff. = 1.33458
[2023-08-21 17:52:30.899] [jointLog] [info] iteration = 500 | max rel diff. = 3.14681
[2023-08-21 17:53:31.838] [jointLog] [info] iteration = 600 | max rel diff. = 0.089202
[2023-08-21 17:54:22.163] [jointLog] [info] iteration = 700 | max rel diff. = 0.16379
[2023-08-21 17:55:16.937] [jointLog] [info] iteration = 800 | max rel diff. = 0.0649479
[2023-08-21 17:56:13.649] [jointLog] [info] iteration = 900 | max rel diff. = 14.4566
[2023-08-21 17:57:20.642] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.427342
[2023-08-21 17:58:15.463] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0294273
[2023-08-21 17:58:44.339] [jointLog] [info] iteration = 1,153 | max rel diff. = 0.00804904
[2023-08-21 17:58:46.509] [jointLog] [info] Finished optimizer
[2023-08-21 17:58:46.509] [jointLog] [info] writing output