[2023-08-22 15:11:28.208] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-22 15:11:28.208] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-22 15:11:28.208] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-22 15:11:28.208] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-22 15:11:28.208] [jointLog] [info] parsing read library format
[2023-08-22 15:11:28.208] [jointLog] [info] There is 1 library.
[2023-08-22 15:11:28.209] [jointLog] [info] Loading pufferfish index
[2023-08-22 15:11:28.209] [jointLog] [info] Loading dense pufferfish index.
[2023-08-22 15:13:18.666] [jointLog] [info] done
[2023-08-22 15:13:18.854] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-22 15:14:06.327] [jointLog] [info] Number of decoys : 194
[2023-08-22 15:14:06.327] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-22 15:14:10.743] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-22 15:23:48.906] [fileLog] [info] 
At end of round 0
==================
Observed 23641601 total fragments (23641601 in most recent round)

[2023-08-22 15:23:48.906] [jointLog] [info] Computed 343,916 rich equivalence classes for further processing
[2023-08-22 15:23:48.906] [jointLog] [info] Counted 21,543,905 total reads in the equivalence classes 
[2023-08-22 15:23:48.918] [jointLog] [info] Number of mappings discarded because of alignment score : 8,503,672
[2023-08-22 15:23:48.918] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,830,834
[2023-08-22 15:23:48.918] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 995,195
[2023-08-22 15:23:48.918] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 520,114
[2023-08-22 15:23:48.918] [jointLog] [info] Mapping rate = 91.1271%

[2023-08-22 15:23:48.918] [jointLog] [info] finished quantifyLibrary()
[2023-08-22 15:23:48.919] [jointLog] [info] Starting optimizer
[2023-08-22 15:23:55.120] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-22 15:23:55.918] [jointLog] [info] iteration = 0 | max rel diff. = 265.648
[2023-08-22 15:24:02.178] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-22 15:31:22.706] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-22 15:31:22.706] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-22 15:32:09.234] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-22 15:32:54.473] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-22 15:33:36.892] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-22 15:34:21.695] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-22 15:35:01.514] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-22 15:35:34.511] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-22 15:36:23.168] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-22 15:37:09.808] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-22 15:37:49.826] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-22 15:38:40.258] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-22 15:38:40.303] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-22 15:39:38.133] [jointLog] [info] iteration = 100 | max rel diff. = 18.197
[2023-08-22 15:40:32.915] [jointLog] [info] iteration = 200 | max rel diff. = 1.38348
[2023-08-22 15:41:20.847] [jointLog] [info] iteration = 300 | max rel diff. = 6.34771
[2023-08-22 15:42:12.931] [jointLog] [info] iteration = 400 | max rel diff. = 0.519294
[2023-08-22 15:43:06.454] [jointLog] [info] iteration = 500 | max rel diff. = 0.05177
[2023-08-22 15:43:57.944] [jointLog] [info] iteration = 600 | max rel diff. = 0.162678
[2023-08-22 15:44:49.468] [jointLog] [info] iteration = 700 | max rel diff. = 0.110942
[2023-08-22 15:45:46.077] [jointLog] [info] iteration = 800 | max rel diff. = 0.0893462
[2023-08-22 15:46:43.490] [jointLog] [info] iteration = 900 | max rel diff. = 0.0145263
[2023-08-22 15:47:34.268] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0556941
[2023-08-22 15:47:44.367] [jointLog] [info] iteration = 1,021 | max rel diff. = 0.00476535
[2023-08-22 15:47:46.609] [jointLog] [info] Finished optimizer
[2023-08-22 15:47:46.609] [jointLog] [info] writing output