[2023-08-25 07:55:19.702] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 07:55:19.702] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 07:55:19.702] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 07:55:19.702] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 07:55:19.702] [jointLog] [info] parsing read library format
[2023-08-25 07:55:19.702] [jointLog] [info] There is 1 library.
[2023-08-25 07:55:19.702] [jointLog] [info] Loading pufferfish index
[2023-08-25 07:55:19.702] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 08:02:48.908] [jointLog] [info] done
[2023-08-25 08:02:49.622] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 08:06:32.787] [jointLog] [info] Number of decoys : 194
[2023-08-25 08:06:32.787] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 08:06:46.159] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 08:06:53.653] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 08:33:46.887] [jointLog] [info] Thread saw mini-batch with a maximum of 7.84% zero probability fragments
[2023-08-25 08:33:47.820] [jointLog] [info] Thread saw mini-batch with a maximum of 7.36% zero probability fragments
[2023-08-25 08:33:47.951] [jointLog] [info] Thread saw mini-batch with a maximum of 7.26% zero probability fragments
[2023-08-25 08:33:48.062] [jointLog] [info] Thread saw mini-batch with a maximum of 7.40% zero probability fragments
[2023-08-25 08:33:48.378] [jointLog] [info] Thread saw mini-batch with a maximum of 7.16% zero probability fragments
[2023-08-25 08:33:48.785] [jointLog] [info] Thread saw mini-batch with a maximum of 7.22% zero probability fragments
[2023-08-25 08:33:48.808] [jointLog] [info] Thread saw mini-batch with a maximum of 7.02% zero probability fragments
[2023-08-25 08:33:48.818] [jointLog] [info] Thread saw mini-batch with a maximum of 7.38% zero probability fragments
[2023-08-25 08:33:51.171] [fileLog] [info] 
At end of round 0
==================
Observed 21340663 total fragments (21340663 in most recent round)

[2023-08-25 08:33:51.170] [jointLog] [info] Computed 345,661 rich equivalence classes for further processing
[2023-08-25 08:33:51.170] [jointLog] [info] Counted 18,228,443 total reads in the equivalence classes 
[2023-08-25 08:33:51.184] [jointLog] [info] Number of mappings discarded because of alignment score : 45,277,421
[2023-08-25 08:33:51.184] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 607,695
[2023-08-25 08:33:51.184] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 326,301
[2023-08-25 08:33:51.184] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 08:33:51.184] [jointLog] [info] Mapping rate = 85.4165%

[2023-08-25 08:33:51.184] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 08:33:51.186] [jointLog] [info] Starting optimizer
[2023-08-25 08:34:18.826] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 08:34:21.501] [jointLog] [info] iteration = 0 | max rel diff. = 301.401
[2023-08-25 08:34:50.156] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 08:46:46.822] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 08:46:46.823] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 08:48:10.016] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 08:49:40.189] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 08:51:02.404] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 08:52:25.041] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 08:53:49.548] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 08:55:09.700] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 08:56:41.202] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 08:58:06.164] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 08:59:34.139] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 09:00:58.721] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 09:04:59.057] [jointLog] [info] iteration = 100 | max rel diff. = 8.75838
[2023-08-25 09:09:38.091] [jointLog] [info] iteration = 200 | max rel diff. = 11.8856
[2023-08-25 09:14:17.831] [jointLog] [info] iteration = 300 | max rel diff. = 6.65367
[2023-08-25 09:14:57.109] [jointLog] [info] iteration = 400 | max rel diff. = 0.724515
[2023-08-25 09:15:32.718] [jointLog] [info] iteration = 500 | max rel diff. = 10.4833
[2023-08-25 09:16:07.940] [jointLog] [info] iteration = 600 | max rel diff. = 0.62156
[2023-08-25 09:16:43.164] [jointLog] [info] iteration = 700 | max rel diff. = 0.579773
[2023-08-25 09:17:17.896] [jointLog] [info] iteration = 800 | max rel diff. = 0.120174
[2023-08-25 09:17:52.837] [jointLog] [info] iteration = 900 | max rel diff. = 0.0307542
[2023-08-25 09:18:27.503] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.681646
[2023-08-25 09:19:02.778] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0548752
[2023-08-25 09:19:15.826] [jointLog] [info] iteration = 1,138 | max rel diff. = 0.00884689
[2023-08-25 09:19:18.064] [jointLog] [info] Finished optimizer
[2023-08-25 09:19:18.064] [jointLog] [info] writing output