[2021-06-30 04:11:22.470] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-06-30 04:11:22.470] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-06-30 04:11:22.470] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-06-30 04:11:22.470] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-06-30 04:11:22.470] [jointLog] [info] parsing read library format
[2021-06-30 04:11:22.470] [jointLog] [info] There is 1 library.
[2021-06-30 04:11:22.609] [jointLog] [info] Loading pufferfish index
[2021-06-30 04:11:22.609] [jointLog] [info] Loading dense pufferfish index.
[2021-06-30 04:13:04.289] [jointLog] [info] done
[2021-06-30 04:13:04.289] [jointLog] [info] Index contained 5,382,683 targets
[2021-06-30 04:13:58.937] [jointLog] [info] Number of decoys : 194
[2021-06-30 04:13:58.937] [jointLog] [info] First decoy index : 5,185,409 
[2021-06-30 04:14:01.702] [jointLog] [info] Automatically detected most likely library type as IU
[2021-06-30 04:16:07.907] [jointLog] [info] Computed 379,717 rich equivalence classes for further processing
[2021-06-30 04:16:07.907] [jointLog] [info] Counted 19,636,108 total reads in the equivalence classes 
[2021-06-30 04:16:07.919] [jointLog] [info] Number of mappings discarded because of alignment score : 3,986,048
[2021-06-30 04:16:07.919] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 400,731
[2021-06-30 04:16:07.919] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 160,527
[2021-06-30 04:16:07.919] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 74,350
[2021-06-30 04:16:07.919] [jointLog] [info] Mapping rate = 93.8905%

[2021-06-30 04:16:07.919] [jointLog] [info] finished quantifyLibrary()
[2021-06-30 04:16:07.919] [jointLog] [info] Starting optimizer
[2021-06-30 04:16:07.908] [fileLog] [info] 
At end of round 0
==================
Observed 20913844 total fragments (20913844 in most recent round)

[2021-06-30 04:16:13.543] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-06-30 04:16:13.911] [jointLog] [info] iteration = 0 | max rel diff. = 623.092
[2021-06-30 04:16:17.513] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-06-30 04:19:59.309] [jointLog] [info] Computed expected counts (for bias correction)
[2021-06-30 04:19:59.310] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-06-30 04:20:17.343] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-06-30 04:20:35.739] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-06-30 04:20:53.753] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-06-30 04:21:12.303] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-06-30 04:21:30.378] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-06-30 04:21:49.104] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-06-30 04:22:07.892] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-06-30 04:22:25.356] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-06-30 04:22:43.885] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-06-30 04:23:02.416] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-06-30 04:23:35.916] [jointLog] [info] iteration = 100 | max rel diff. = 18.3123
[2021-06-30 04:24:12.737] [jointLog] [info] iteration = 200 | max rel diff. = 15.4189
[2021-06-30 04:24:49.786] [jointLog] [info] iteration = 300 | max rel diff. = 0.418427
[2021-06-30 04:25:26.939] [jointLog] [info] iteration = 400 | max rel diff. = 1.14168
[2021-06-30 04:26:03.897] [jointLog] [info] iteration = 500 | max rel diff. = 3.54287
[2021-06-30 04:26:40.925] [jointLog] [info] iteration = 600 | max rel diff. = 1.93819
[2021-06-30 04:27:17.967] [jointLog] [info] iteration = 700 | max rel diff. = 0.237829
[2021-06-30 04:27:55.558] [jointLog] [info] iteration = 800 | max rel diff. = 0.368151
[2021-06-30 04:28:32.564] [jointLog] [info] iteration = 900 | max rel diff. = 0.52165
[2021-06-30 04:29:09.603] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0498546
[2021-06-30 04:29:46.645] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.148088
[2021-06-30 04:30:23.911] [jointLog] [info] iteration = 1,200 | max rel diff. = 4.06473
[2021-06-30 04:31:01.049] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.182983
[2021-06-30 04:31:38.700] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0502582
[2021-06-30 04:32:16.458] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0393384
[2021-06-30 04:32:26.659] [jointLog] [info] iteration = 1,528 | max rel diff. = 0.00939604
[2021-06-30 04:32:28.885] [jointLog] [info] Finished optimizer
[2021-06-30 04:32:28.885] [jointLog] [info] writing output