[2022-12-20 23:41:46.079] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:41:46.079] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:41:46.079] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:41:46.079] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:41:46.079] [jointLog] [info] parsing read library format
[2022-12-20 23:41:46.079] [jointLog] [info] There is 1 library.
[2022-12-20 23:41:46.079] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:41:46.079] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:42:06.625] [jointLog] [info] done
[2022-12-20 23:42:06.679] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:42:07.001] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:42:07.001] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:42:08.005] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:45:35.523] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:45:35.551] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:45:35.716] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:45:35.743] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:45:35.784] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:45:35.810] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:45:35.873] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:45:35.928] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:45:36.172] [fileLog] [info] 
At end of round 0
==================
Observed 17364806 total fragments (17364806 in most recent round)

[2022-12-20 23:45:36.171] [jointLog] [info] Computed 262,966 rich equivalence classes for further processing
[2022-12-20 23:45:36.171] [jointLog] [info] Counted 13,969,702 total reads in the equivalence classes 
[2022-12-20 23:45:36.177] [jointLog] [info] Number of mappings discarded because of alignment score : 25,099,535
[2022-12-20 23:45:36.177] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,816,259
[2022-12-20 23:45:36.177] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 354,014
[2022-12-20 23:45:36.177] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,052,047
[2022-12-20 23:45:36.177] [jointLog] [info] Mapping rate = 80.4484%

[2022-12-20 23:45:36.177] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:45:36.200] [jointLog] [info] Starting optimizer
[2022-12-20 23:45:36.301] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:45:36.315] [jointLog] [info] iteration = 0 | max rel diff. = 6738.44
[2022-12-20 23:45:36.461] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:45:37.773] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:45:37.773] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-20 23:45:38.601] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:45:39.597] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:45:40.453] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-20 23:45:41.307] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:45:42.189] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:45:43.059] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:45:44.017] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:45:44.905] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-20 23:45:45.692] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:45:46.636] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:45:46.637] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:45:47.944] [jointLog] [info] iteration = 100 | max rel diff. = 19.5182
[2022-12-20 23:45:49.415] [jointLog] [info] iteration = 200 | max rel diff. = 13.2334
[2022-12-20 23:45:50.870] [jointLog] [info] iteration = 300 | max rel diff. = 1.75295
[2022-12-20 23:45:52.406] [jointLog] [info] iteration = 400 | max rel diff. = 0.260839
[2022-12-20 23:45:53.869] [jointLog] [info] iteration = 500 | max rel diff. = 0.607874
[2022-12-20 23:45:55.280] [jointLog] [info] iteration = 600 | max rel diff. = 0.120574
[2022-12-20 23:45:56.687] [jointLog] [info] iteration = 700 | max rel diff. = 0.49507
[2022-12-20 23:45:58.122] [jointLog] [info] iteration = 800 | max rel diff. = 0.0229566
[2022-12-20 23:45:59.564] [jointLog] [info] iteration = 900 | max rel diff. = 0.0867128
[2022-12-20 23:46:00.982] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.177284
[2022-12-20 23:46:02.421] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.126216
[2022-12-20 23:46:03.837] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0678411
[2022-12-20 23:46:05.302] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0315198
[2022-12-20 23:46:06.713] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.031406
[2022-12-20 23:46:07.829] [jointLog] [info] iteration = 1,479 | max rel diff. = 0.00484706
[2022-12-20 23:46:07.849] [jointLog] [info] Finished optimizer
[2022-12-20 23:46:07.849] [jointLog] [info] writing output