[2023-08-27 15:41:12.152] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 15:41:12.152] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 15:41:12.152] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 15:41:12.152] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 15:41:12.152] [jointLog] [info] parsing read library format
[2023-08-27 15:41:12.152] [jointLog] [info] There is 1 library.
[2023-08-27 15:41:12.152] [jointLog] [info] Loading pufferfish index
[2023-08-27 15:41:12.152] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 15:42:34.709] [jointLog] [info] done
[2023-08-27 15:42:34.823] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 15:43:10.940] [jointLog] [info] Number of decoys : 194
[2023-08-27 15:43:10.940] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 15:43:13.396] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-27 15:49:07.019] [jointLog] [info] Computed 223,890 rich equivalence classes for further processing
[2023-08-27 15:49:07.019] [jointLog] [info] Counted 25,436,610 total reads in the equivalence classes 
[2023-08-27 15:49:07.027] [jointLog] [info] Number of mappings discarded because of alignment score : 9,665,084
[2023-08-27 15:49:07.027] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,533,702
[2023-08-27 15:49:07.027] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 744,787
[2023-08-27 15:49:07.027] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 770,495
[2023-08-27 15:49:07.027] [jointLog] [info] Mapping rate = 93.0054%

[2023-08-27 15:49:07.027] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 15:49:07.027] [jointLog] [info] Starting optimizer
[2023-08-27 15:49:07.020] [fileLog] [info] 
At end of round 0
==================
Observed 27349597 total fragments (27349597 in most recent round)

[2023-08-27 15:49:16.290] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 15:49:16.625] [jointLog] [info] iteration = 0 | max rel diff. = 258.868
[2023-08-27 15:49:19.966] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 15:52:27.053] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 15:52:27.053] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 15:52:42.212] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 15:52:57.356] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 15:53:12.609] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 15:53:28.899] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 15:53:44.677] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 15:53:59.988] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 15:54:15.671] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 15:54:30.877] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 15:54:45.609] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 15:55:00.686] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 15:55:00.713] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 15:55:31.351] [jointLog] [info] iteration = 100 | max rel diff. = 17.3206
[2023-08-27 15:56:05.547] [jointLog] [info] iteration = 200 | max rel diff. = 5.37522
[2023-08-27 15:56:38.963] [jointLog] [info] iteration = 300 | max rel diff. = 0.376771
[2023-08-27 15:57:12.540] [jointLog] [info] iteration = 400 | max rel diff. = 0.679642
[2023-08-27 15:57:45.429] [jointLog] [info] iteration = 500 | max rel diff. = 0.651069
[2023-08-27 15:58:18.579] [jointLog] [info] iteration = 600 | max rel diff. = 0.0157692
[2023-08-27 15:58:52.296] [jointLog] [info] iteration = 700 | max rel diff. = 0.144996
[2023-08-27 15:59:25.730] [jointLog] [info] iteration = 800 | max rel diff. = 1.80769
[2023-08-27 15:59:59.381] [jointLog] [info] iteration = 900 | max rel diff. = 0.302275
[2023-08-27 16:00:33.893] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.139706
[2023-08-27 16:01:06.386] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.440184
[2023-08-27 16:01:40.097] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.256529
[2023-08-27 16:02:13.619] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.304639
[2023-08-27 16:02:46.954] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0379428
[2023-08-27 16:03:19.949] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0581342
[2023-08-27 16:03:40.266] [jointLog] [info] iteration = 1,563 | max rel diff. = 0.0060291
[2023-08-27 16:03:41.843] [jointLog] [info] Finished optimizer
[2023-08-27 16:03:41.843] [jointLog] [info] writing output