[2023-08-22 10:27:17.519] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-22 10:27:17.519] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-22 10:27:17.519] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-22 10:27:17.519] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-22 10:27:17.519] [jointLog] [info] parsing read library format
[2023-08-22 10:27:17.519] [jointLog] [info] There is 1 library.
[2023-08-22 10:27:17.519] [jointLog] [info] Loading pufferfish index
[2023-08-22 10:27:17.519] [jointLog] [info] Loading dense pufferfish index.
[2023-08-22 10:30:02.103] [jointLog] [info] done
[2023-08-22 10:30:02.354] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-22 10:31:16.437] [jointLog] [info] Number of decoys : 194
[2023-08-22 10:31:16.437] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-22 10:31:22.124] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-22 10:43:59.718] [jointLog] [info] Computed 346,944 rich equivalence classes for further processing
[2023-08-22 10:43:59.718] [jointLog] [info] Counted 25,513,880 total reads in the equivalence classes 
[2023-08-22 10:43:59.729] [jointLog] [info] Number of mappings discarded because of alignment score : 10,819,212
[2023-08-22 10:43:59.729] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,125,554
[2023-08-22 10:43:59.729] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,106,797
[2023-08-22 10:43:59.729] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 954,806
[2023-08-22 10:43:59.729] [jointLog] [info] Mapping rate = 91.2362%

[2023-08-22 10:43:59.730] [jointLog] [info] finished quantifyLibrary()
[2023-08-22 10:43:59.730] [jointLog] [info] Starting optimizer
[2023-08-22 10:43:59.719] [fileLog] [info] 
At end of round 0
==================
Observed 27964640 total fragments (27964640 in most recent round)

[2023-08-22 10:44:05.141] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-22 10:44:05.602] [jointLog] [info] iteration = 0 | max rel diff. = 269.184
[2023-08-22 10:44:11.104] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-22 10:50:22.019] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-22 10:50:22.020] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-22 10:51:06.961] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-22 10:51:44.596] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-22 10:52:20.509] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-22 10:53:05.583] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-22 10:53:44.162] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-22 10:54:19.826] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-22 10:54:56.723] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-22 10:55:32.141] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-22 10:56:07.206] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-22 10:56:44.620] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-22 10:57:29.456] [jointLog] [info] iteration = 100 | max rel diff. = 13.0654
[2023-08-22 10:58:28.288] [jointLog] [info] iteration = 200 | max rel diff. = 2.08037
[2023-08-22 10:59:25.178] [jointLog] [info] iteration = 300 | max rel diff. = 5.14983
[2023-08-22 11:00:18.185] [jointLog] [info] iteration = 400 | max rel diff. = 0.286208
[2023-08-22 11:01:08.661] [jointLog] [info] iteration = 500 | max rel diff. = 0.109668
[2023-08-22 11:02:00.964] [jointLog] [info] iteration = 600 | max rel diff. = 10.4366
[2023-08-22 11:02:42.114] [jointLog] [info] iteration = 700 | max rel diff. = 1.02509
[2023-08-22 11:03:22.929] [jointLog] [info] iteration = 800 | max rel diff. = 0.109936
[2023-08-22 11:04:07.948] [jointLog] [info] iteration = 900 | max rel diff. = 0.0178095
[2023-08-22 11:04:52.180] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0326034
[2023-08-22 11:05:05.951] [jointLog] [info] iteration = 1,031 | max rel diff. = 0.00382193
[2023-08-22 11:05:08.306] [jointLog] [info] Finished optimizer
[2023-08-22 11:05:08.306] [jointLog] [info] writing output