[2023-08-30 19:46:13.025] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-30 19:46:13.025] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-30 19:46:13.025] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-30 19:46:13.025] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-30 19:46:13.025] [jointLog] [info] parsing read library format
[2023-08-30 19:46:13.025] [jointLog] [info] There is 1 library.
[2023-08-30 19:46:13.026] [jointLog] [info] Loading pufferfish index
[2023-08-30 19:46:13.026] [jointLog] [info] Loading dense pufferfish index.
[2023-08-30 19:48:03.386] [jointLog] [info] done
[2023-08-30 19:48:03.628] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-30 19:48:56.607] [jointLog] [info] Number of decoys : 194
[2023-08-30 19:48:56.607] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-30 19:49:01.030] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-30 20:04:35.030] [jointLog] [info] Thread saw mini-batch with a maximum of 13.18% zero probability fragments
[2023-08-30 20:04:35.114] [jointLog] [info] Thread saw mini-batch with a maximum of 13.36% zero probability fragments
[2023-08-30 20:04:35.238] [jointLog] [info] Thread saw mini-batch with a maximum of 13.12% zero probability fragments
[2023-08-30 20:04:35.249] [jointLog] [info] Thread saw mini-batch with a maximum of 13.12% zero probability fragments
[2023-08-30 20:04:35.319] [jointLog] [info] Thread saw mini-batch with a maximum of 13.34% zero probability fragments
[2023-08-30 20:04:35.359] [jointLog] [info] Thread saw mini-batch with a maximum of 13.10% zero probability fragments
[2023-08-30 20:04:35.413] [jointLog] [info] Thread saw mini-batch with a maximum of 13.28% zero probability fragments
[2023-08-30 20:04:35.573] [jointLog] [info] Thread saw mini-batch with a maximum of 13.16% zero probability fragments
[2023-08-30 20:04:36.131] [jointLog] [info] Computed 255,212 rich equivalence classes for further processing
[2023-08-30 20:04:36.131] [jointLog] [info] Counted 34,921,145 total reads in the equivalence classes 
[2023-08-30 20:04:36.138] [jointLog] [info] Number of mappings discarded because of alignment score : 15,734,071
[2023-08-30 20:04:36.138] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,214,177
[2023-08-30 20:04:36.138] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,115,235
[2023-08-30 20:04:36.138] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 670,212
[2023-08-30 20:04:36.138] [jointLog] [info] Mapping rate = 81.0298%

[2023-08-30 20:04:36.138] [jointLog] [info] finished quantifyLibrary()
[2023-08-30 20:04:36.139] [jointLog] [info] Starting optimizer
[2023-08-30 20:04:36.132] [fileLog] [info] 
At end of round 0
==================
Observed 43096651 total fragments (43096651 in most recent round)

[2023-08-30 20:04:46.139] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-30 20:04:46.513] [jointLog] [info] iteration = 0 | max rel diff. = 249.98
[2023-08-30 20:04:50.293] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-30 20:10:22.656] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-30 20:10:22.657] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-30 20:10:55.707] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-30 20:11:29.395] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-30 20:12:01.992] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-30 20:12:35.935] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-30 20:12:59.767] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-30 20:13:22.544] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-30 20:13:54.964] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-30 20:14:27.560] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-30 20:15:00.180] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-30 20:15:34.860] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 20:15:34.868] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 20:16:07.564] [jointLog] [info] iteration = 100 | max rel diff. = 20.048
[2023-08-30 20:16:43.436] [jointLog] [info] iteration = 200 | max rel diff. = 4.30151
[2023-08-30 20:17:20.151] [jointLog] [info] iteration = 300 | max rel diff. = 2.27128
[2023-08-30 20:17:54.116] [jointLog] [info] iteration = 400 | max rel diff. = 0.339716
[2023-08-30 20:18:29.925] [jointLog] [info] iteration = 500 | max rel diff. = 0.927554
[2023-08-30 20:19:06.090] [jointLog] [info] iteration = 600 | max rel diff. = 0.153527
[2023-08-30 20:19:42.920] [jointLog] [info] iteration = 700 | max rel diff. = 0.0807382
[2023-08-30 20:20:19.007] [jointLog] [info] iteration = 800 | max rel diff. = 0.358654
[2023-08-30 20:20:55.156] [jointLog] [info] iteration = 900 | max rel diff. = 0.609085
[2023-08-30 20:21:28.485] [jointLog] [info] iteration = 992 | max rel diff. = 0.00655262
[2023-08-30 20:21:30.202] [jointLog] [info] Finished optimizer
[2023-08-30 20:21:30.202] [jointLog] [info] writing output