[2023-08-29 12:27:32.188] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-29 12:27:32.188] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-29 12:27:32.188] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-29 12:27:32.188] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-29 12:27:32.188] [jointLog] [info] parsing read library format
[2023-08-29 12:27:32.188] [jointLog] [info] There is 1 library.
[2023-08-29 12:27:32.188] [jointLog] [info] Loading pufferfish index
[2023-08-29 12:27:32.188] [jointLog] [info] Loading dense pufferfish index.
[2023-08-29 12:28:53.030] [jointLog] [info] done
[2023-08-29 12:28:53.182] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-29 12:29:32.333] [jointLog] [info] Number of decoys : 194
[2023-08-29 12:29:32.333] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-29 12:29:36.004] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-29 12:38:05.443] [fileLog] [info] 
At end of round 0
==================
Observed 30283667 total fragments (30283667 in most recent round)

[2023-08-29 12:38:05.442] [jointLog] [info] Computed 292,328 rich equivalence classes for further processing
[2023-08-29 12:38:05.442] [jointLog] [info] Counted 27,797,225 total reads in the equivalence classes 
[2023-08-29 12:38:05.455] [jointLog] [info] Number of mappings discarded because of alignment score : 11,949,175
[2023-08-29 12:38:05.455] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,107,434
[2023-08-29 12:38:05.455] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,076,697
[2023-08-29 12:38:05.455] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 446,851
[2023-08-29 12:38:05.455] [jointLog] [info] Mapping rate = 91.7895%

[2023-08-29 12:38:05.455] [jointLog] [info] finished quantifyLibrary()
[2023-08-29 12:38:05.455] [jointLog] [info] Starting optimizer
[2023-08-29 12:38:10.872] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-29 12:38:11.228] [jointLog] [info] iteration = 0 | max rel diff. = 254.046
[2023-08-29 12:38:14.807] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-29 12:42:37.056] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-29 12:42:37.056] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-29 12:43:00.163] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-29 12:43:22.044] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-29 12:43:43.758] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-29 12:44:06.072] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-29 12:44:27.801] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-29 12:44:49.572] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-29 12:45:11.769] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-29 12:45:34.366] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-29 12:45:56.144] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-29 12:46:18.822] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-29 12:46:50.329] [jointLog] [info] iteration = 100 | max rel diff. = 2.30538
[2023-08-29 12:47:25.383] [jointLog] [info] iteration = 200 | max rel diff. = 5.39558
[2023-08-29 12:48:00.099] [jointLog] [info] iteration = 300 | max rel diff. = 0.114258
[2023-08-29 12:48:34.215] [jointLog] [info] iteration = 400 | max rel diff. = 0.250342
[2023-08-29 12:49:08.592] [jointLog] [info] iteration = 500 | max rel diff. = 0.0567281
[2023-08-29 12:49:42.695] [jointLog] [info] iteration = 600 | max rel diff. = 0.166877
[2023-08-29 12:50:17.822] [jointLog] [info] iteration = 700 | max rel diff. = 0.0384363
[2023-08-29 12:50:52.070] [jointLog] [info] iteration = 800 | max rel diff. = 0.012304
[2023-08-29 12:51:26.323] [jointLog] [info] iteration = 900 | max rel diff. = 0.0539869
[2023-08-29 12:52:01.105] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0678929
[2023-08-29 12:52:06.916] [jointLog] [info] iteration = 1,017 | max rel diff. = 0.00582402
[2023-08-29 12:52:08.904] [jointLog] [info] Finished optimizer
[2023-08-29 12:52:08.904] [jointLog] [info] writing output