[2023-08-25 13:53:52.477] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 13:53:52.477] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 13:53:52.477] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 13:53:52.477] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 13:53:52.477] [jointLog] [info] parsing read library format
[2023-08-25 13:53:52.477] [jointLog] [info] There is 1 library.
[2023-08-25 13:53:52.477] [jointLog] [info] Loading pufferfish index
[2023-08-25 13:53:52.477] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 13:55:09.193] [jointLog] [info] done
[2023-08-25 13:55:09.317] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 13:55:44.417] [jointLog] [info] Number of decoys : 194
[2023-08-25 13:55:44.417] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 13:55:46.518] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-25 14:01:55.031] [fileLog] [info] 
At end of round 0
==================
Observed 26032584 total fragments (26032584 in most recent round)

[2023-08-25 14:01:55.030] [jointLog] [info] Computed 352,033 rich equivalence classes for further processing
[2023-08-25 14:01:55.030] [jointLog] [info] Counted 23,705,336 total reads in the equivalence classes 
[2023-08-25 14:01:55.040] [jointLog] [info] Number of mappings discarded because of alignment score : 12,398,470
[2023-08-25 14:01:55.040] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,105,003
[2023-08-25 14:01:55.040] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 665,840
[2023-08-25 14:01:55.040] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 763,365
[2023-08-25 14:01:55.040] [jointLog] [info] Mapping rate = 91.0602%

[2023-08-25 14:01:55.040] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 14:01:55.040] [jointLog] [info] Starting optimizer
[2023-08-25 14:01:59.602] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 14:01:59.938] [jointLog] [info] iteration = 0 | max rel diff. = 272.358
[2023-08-25 14:02:03.397] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 14:07:31.125] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 14:07:31.126] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 14:07:56.732] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 14:08:23.396] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 14:08:50.148] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 14:09:17.529] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 14:09:43.660] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 14:10:10.814] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 14:10:36.519] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 14:11:03.171] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 14:11:30.489] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 14:11:56.543] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 14:12:26.890] [jointLog] [info] iteration = 100 | max rel diff. = 7.03667
[2023-08-25 14:13:01.205] [jointLog] [info] iteration = 200 | max rel diff. = 9.65865
[2023-08-25 14:13:34.627] [jointLog] [info] iteration = 300 | max rel diff. = 0.91531
[2023-08-25 14:14:08.023] [jointLog] [info] iteration = 400 | max rel diff. = 0.158857
[2023-08-25 14:14:41.370] [jointLog] [info] iteration = 500 | max rel diff. = 0.65658
[2023-08-25 14:15:14.611] [jointLog] [info] iteration = 600 | max rel diff. = 0.294796
[2023-08-25 14:15:48.126] [jointLog] [info] iteration = 700 | max rel diff. = 0.100679
[2023-08-25 14:16:21.162] [jointLog] [info] iteration = 800 | max rel diff. = 0.322201
[2023-08-25 14:16:31.341] [jointLog] [info] iteration = 832 | max rel diff. = 0.00984305
[2023-08-25 14:16:33.329] [jointLog] [info] Finished optimizer
[2023-08-25 14:16:33.329] [jointLog] [info] writing output