[2023-08-28 18:34:48.161] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 18:34:48.161] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 18:34:48.161] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 18:34:48.161] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 18:34:48.161] [jointLog] [info] parsing read library format
[2023-08-28 18:34:48.161] [jointLog] [info] There is 1 library.
[2023-08-28 18:34:48.161] [jointLog] [info] Loading pufferfish index
[2023-08-28 18:34:48.161] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 18:36:53.432] [jointLog] [info] done
[2023-08-28 18:36:53.651] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 18:37:52.594] [jointLog] [info] Number of decoys : 194
[2023-08-28 18:37:52.594] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 18:37:57.616] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-28 18:44:24.707] [jointLog] [info] Thread saw mini-batch with a maximum of 25.16% zero probability fragments
[2023-08-28 18:44:24.794] [jointLog] [info] Thread saw mini-batch with a maximum of 24.96% zero probability fragments
[2023-08-28 18:44:25.058] [jointLog] [info] Thread saw mini-batch with a maximum of 25.37% zero probability fragments
[2023-08-28 18:44:25.133] [jointLog] [info] Thread saw mini-batch with a maximum of 25.10% zero probability fragments
[2023-08-28 18:44:25.350] [jointLog] [info] Thread saw mini-batch with a maximum of 24.96% zero probability fragments
[2023-08-28 18:44:25.636] [jointLog] [info] Thread saw mini-batch with a maximum of 25.08% zero probability fragments
[2023-08-28 18:44:25.883] [jointLog] [info] Thread saw mini-batch with a maximum of 25.28% zero probability fragments
[2023-08-28 18:44:25.886] [jointLog] [info] Thread saw mini-batch with a maximum of 25.38% zero probability fragments
[2023-08-28 18:44:26.676] [jointLog] [info] Computed 302,309 rich equivalence classes for further processing
[2023-08-28 18:44:26.676] [jointLog] [info] Counted 7,860,805 total reads in the equivalence classes 
[2023-08-28 18:44:26.689] [jointLog] [info] Number of mappings discarded because of alignment score : 22,080,121
[2023-08-28 18:44:26.689] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,455,489
[2023-08-28 18:44:26.689] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 458,642
[2023-08-28 18:44:26.689] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,266,852
[2023-08-28 18:44:26.689] [jointLog] [info] Mapping rate = 63.4627%

[2023-08-28 18:44:26.689] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 18:44:26.691] [jointLog] [info] Starting optimizer
[2023-08-28 18:44:26.677] [fileLog] [info] 
At end of round 0
==================
Observed 12386490 total fragments (12386490 in most recent round)

[2023-08-28 18:44:32.881] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 18:44:33.361] [jointLog] [info] iteration = 0 | max rel diff. = 166.291
[2023-08-28 18:44:38.497] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 18:49:35.415] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 18:49:35.416] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 18:50:05.115] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 18:50:34.957] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 18:51:04.458] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 18:51:36.061] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 18:52:04.991] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 18:52:35.128] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 18:53:05.022] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 18:53:37.640] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 18:54:05.669] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 18:54:30.577] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 18:54:30.664] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 18:55:13.350] [jointLog] [info] iteration = 100 | max rel diff. = 8.18614
[2023-08-28 18:56:00.691] [jointLog] [info] iteration = 200 | max rel diff. = 8.30027
[2023-08-28 18:56:48.500] [jointLog] [info] iteration = 300 | max rel diff. = 0.618455
[2023-08-28 18:57:36.133] [jointLog] [info] iteration = 400 | max rel diff. = 0.0469129
[2023-08-28 18:58:23.784] [jointLog] [info] iteration = 500 | max rel diff. = 0.919229
[2023-08-28 18:59:09.799] [jointLog] [info] iteration = 600 | max rel diff. = 0.249372
[2023-08-28 18:59:58.295] [jointLog] [info] iteration = 700 | max rel diff. = 0.26325
[2023-08-28 19:00:43.586] [jointLog] [info] iteration = 800 | max rel diff. = 0.243717
[2023-08-28 19:01:32.624] [jointLog] [info] iteration = 900 | max rel diff. = 1.46752
[2023-08-28 19:01:53.403] [jointLog] [info] iteration = 947 | max rel diff. = 0.00928881
[2023-08-28 19:01:55.583] [jointLog] [info] Finished optimizer
[2023-08-28 19:01:55.583] [jointLog] [info] writing output