[2023-08-29 11:57:47.043] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-29 11:57:47.043] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-29 11:57:47.043] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-29 11:57:47.043] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-29 11:57:47.043] [jointLog] [info] parsing read library format
[2023-08-29 11:57:47.043] [jointLog] [info] There is 1 library.
[2023-08-29 11:57:47.044] [jointLog] [info] Loading pufferfish index
[2023-08-29 11:57:47.044] [jointLog] [info] Loading dense pufferfish index.
[2023-08-29 11:59:15.352] [jointLog] [info] done
[2023-08-29 11:59:15.486] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-29 11:59:57.197] [jointLog] [info] Number of decoys : 194
[2023-08-29 11:59:57.197] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-29 11:59:59.930] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-29 12:08:28.632] [fileLog] [info] 
At end of round 0
==================
Observed 27802447 total fragments (27802447 in most recent round)

[2023-08-29 12:08:28.632] [jointLog] [info] Computed 320,340 rich equivalence classes for further processing
[2023-08-29 12:08:28.632] [jointLog] [info] Counted 25,365,915 total reads in the equivalence classes 
[2023-08-29 12:08:28.639] [jointLog] [info] Number of mappings discarded because of alignment score : 10,007,162
[2023-08-29 12:08:28.639] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,069,125
[2023-08-29 12:08:28.639] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,101,519
[2023-08-29 12:08:28.639] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 374,336
[2023-08-29 12:08:28.639] [jointLog] [info] Mapping rate = 91.2363%

[2023-08-29 12:08:28.639] [jointLog] [info] finished quantifyLibrary()
[2023-08-29 12:08:28.640] [jointLog] [info] Starting optimizer
[2023-08-29 12:08:32.519] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-29 12:08:32.875] [jointLog] [info] iteration = 0 | max rel diff. = 248.906
[2023-08-29 12:08:36.468] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-29 12:13:29.839] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-29 12:13:29.839] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-29 12:13:52.556] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-29 12:14:19.146] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-29 12:14:46.068] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-29 12:15:15.263] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-29 12:15:41.088] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-29 12:16:08.517] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-29 12:16:36.763] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-29 12:17:02.321] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-29 12:17:31.627] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-29 12:17:58.356] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-29 12:18:31.036] [jointLog] [info] iteration = 100 | max rel diff. = 6.10127
[2023-08-29 12:19:07.437] [jointLog] [info] iteration = 200 | max rel diff. = 2.09815
[2023-08-29 12:19:44.119] [jointLog] [info] iteration = 300 | max rel diff. = 0.743922
[2023-08-29 12:20:20.750] [jointLog] [info] iteration = 400 | max rel diff. = 0.213344
[2023-08-29 12:20:56.093] [jointLog] [info] iteration = 500 | max rel diff. = 0.0964117
[2023-08-29 12:21:31.894] [jointLog] [info] iteration = 600 | max rel diff. = 0.143452
[2023-08-29 12:22:07.607] [jointLog] [info] iteration = 700 | max rel diff. = 0.280199
[2023-08-29 12:22:43.360] [jointLog] [info] iteration = 800 | max rel diff. = 0.0157064
[2023-08-29 12:23:18.114] [jointLog] [info] iteration = 900 | max rel diff. = 0.0329019
[2023-08-29 12:23:46.924] [jointLog] [info] iteration = 982 | max rel diff. = 0.00581121
[2023-08-29 12:23:48.710] [jointLog] [info] Finished optimizer
[2023-08-29 12:23:48.710] [jointLog] [info] writing output