[2023-08-25 23:23:01.380] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 23:23:01.380] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 23:23:01.380] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 23:23:01.380] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 23:23:01.380] [jointLog] [info] parsing read library format
[2023-08-25 23:23:01.380] [jointLog] [info] There is 1 library.
[2023-08-25 23:23:01.381] [jointLog] [info] Loading pufferfish index
[2023-08-25 23:23:01.381] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 23:24:12.828] [jointLog] [info] done
[2023-08-25 23:24:12.956] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 23:24:47.604] [jointLog] [info] Number of decoys : 194
[2023-08-25 23:24:47.604] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 23:24:50.759] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-25 23:33:49.556] [jointLog] [info] Thread saw mini-batch with a maximum of 11.16% zero probability fragments
[2023-08-25 23:33:49.605] [jointLog] [info] Thread saw mini-batch with a maximum of 10.96% zero probability fragments
[2023-08-25 23:33:49.687] [jointLog] [info] Thread saw mini-batch with a maximum of 11.02% zero probability fragments
[2023-08-25 23:33:49.698] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2023-08-25 23:33:49.752] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2023-08-25 23:33:49.758] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2023-08-25 23:33:50.085] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2023-08-25 23:33:50.130] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2023-08-25 23:33:50.806] [fileLog] [info] 
At end of round 0
==================
Observed 33152136 total fragments (33152136 in most recent round)

[2023-08-25 23:33:50.805] [jointLog] [info] Computed 468,817 rich equivalence classes for further processing
[2023-08-25 23:33:50.805] [jointLog] [info] Counted 26,196,875 total reads in the equivalence classes 
[2023-08-25 23:33:50.815] [jointLog] [info] Number of mappings discarded because of alignment score : 23,896,256
[2023-08-25 23:33:50.815] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,836,214
[2023-08-25 23:33:50.815] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,548,970
[2023-08-25 23:33:50.815] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,587,948
[2023-08-25 23:33:50.815] [jointLog] [info] Mapping rate = 79.0202%

[2023-08-25 23:33:50.815] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 23:33:50.817] [jointLog] [info] Starting optimizer
[2023-08-25 23:33:56.625] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 23:33:56.981] [jointLog] [info] iteration = 0 | max rel diff. = 376.214
[2023-08-25 23:34:00.584] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 23:39:01.742] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 23:39:01.743] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 23:39:27.551] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 23:39:53.762] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 23:40:19.170] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 23:40:45.681] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 23:41:10.669] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 23:41:36.714] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 23:42:02.508] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 23:42:26.104] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 23:42:50.927] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 23:43:15.356] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 23:43:15.398] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 23:43:50.204] [jointLog] [info] iteration = 100 | max rel diff. = 14.3268
[2023-08-25 23:44:28.015] [jointLog] [info] iteration = 200 | max rel diff. = 2.79319
[2023-08-25 23:45:05.243] [jointLog] [info] iteration = 300 | max rel diff. = 1.63214
[2023-08-25 23:45:42.772] [jointLog] [info] iteration = 400 | max rel diff. = 0.643531
[2023-08-25 23:46:19.964] [jointLog] [info] iteration = 500 | max rel diff. = 0.935673
[2023-08-25 23:46:56.525] [jointLog] [info] iteration = 600 | max rel diff. = 0.111455
[2023-08-25 23:47:33.273] [jointLog] [info] iteration = 700 | max rel diff. = 0.348643
[2023-08-25 23:48:09.350] [jointLog] [info] iteration = 800 | max rel diff. = 0.111513
[2023-08-25 23:48:45.457] [jointLog] [info] iteration = 900 | max rel diff. = 0.0884334
[2023-08-25 23:49:21.610] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0228676
[2023-08-25 23:49:57.657] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.15828
[2023-08-25 23:50:33.911] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0176345
[2023-08-25 23:51:09.921] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.361881
[2023-08-25 23:51:46.219] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.166579
[2023-08-25 23:51:58.079] [jointLog] [info] iteration = 1,434 | max rel diff. = 0.00627103
[2023-08-25 23:52:00.693] [jointLog] [info] Finished optimizer
[2023-08-25 23:52:00.693] [jointLog] [info] writing output