[2023-09-16 15:45:40.434] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 15:45:40.434] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 15:45:40.434] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 15:45:40.434] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 15:45:40.434] [jointLog] [info] parsing read library format
[2023-09-16 15:45:40.434] [jointLog] [info] There is 1 library.
[2023-09-16 15:45:40.434] [jointLog] [info] Loading pufferfish index
[2023-09-16 15:45:40.434] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 15:46:52.937] [jointLog] [info] done
[2023-09-16 15:46:53.078] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 15:47:28.749] [jointLog] [info] Number of decoys : 194
[2023-09-16 15:47:28.749] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 15:47:31.057] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 15:47:31.994] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 15:48:10.004] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments
[2023-09-16 15:48:10.027] [jointLog] [info] Thread saw mini-batch with a maximum of 5.24% zero probability fragments
[2023-09-16 15:48:10.037] [jointLog] [info] Thread saw mini-batch with a maximum of 4.82% zero probability fragments
[2023-09-16 15:48:10.108] [jointLog] [info] Thread saw mini-batch with a maximum of 4.76% zero probability fragments
[2023-09-16 15:48:10.118] [jointLog] [info] Thread saw mini-batch with a maximum of 4.66% zero probability fragments
[2023-09-16 15:48:10.131] [jointLog] [info] Thread saw mini-batch with a maximum of 4.78% zero probability fragments
[2023-09-16 15:48:10.212] [jointLog] [info] Thread saw mini-batch with a maximum of 5.14% zero probability fragments
[2023-09-16 15:48:10.233] [jointLog] [info] Thread saw mini-batch with a maximum of 4.84% zero probability fragments
[2023-09-16 15:48:10.502] [jointLog] [info] Computed 209,439 rich equivalence classes for further processing
[2023-09-16 15:48:10.502] [jointLog] [info] Counted 5,425,351 total reads in the equivalence classes 
[2023-09-16 15:48:10.512] [jointLog] [info] Number of mappings discarded because of alignment score : 9,117,591
[2023-09-16 15:48:10.512] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 55,120
[2023-09-16 15:48:10.512] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 40,685
[2023-09-16 15:48:10.512] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 15:48:10.512] [jointLog] [info] Mapping rate = 90.6109%

[2023-09-16 15:48:10.512] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 15:48:10.513] [jointLog] [info] Starting optimizer
[2023-09-16 15:48:10.503] [fileLog] [info] 
At end of round 0
==================
Observed 5987523 total fragments (5987523 in most recent round)

[2023-09-16 15:48:14.670] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 15:48:15.020] [jointLog] [info] iteration = 0 | max rel diff. = 118.705
[2023-09-16 15:48:18.569] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 15:49:30.646] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 15:49:30.646] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 15:49:37.529] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 15:49:44.062] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 15:49:50.571] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 15:49:57.459] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 15:50:04.122] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 15:50:10.956] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 15:50:17.808] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 15:50:24.388] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 15:50:31.091] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 15:50:37.765] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 15:51:08.946] [jointLog] [info] iteration = 100 | max rel diff. = 18.1892
[2023-09-16 15:51:42.838] [jointLog] [info] iteration = 200 | max rel diff. = 7.15734
[2023-09-16 15:52:18.059] [jointLog] [info] iteration = 300 | max rel diff. = 6.76442
[2023-09-16 15:52:53.190] [jointLog] [info] iteration = 400 | max rel diff. = 1.82835
[2023-09-16 15:53:28.095] [jointLog] [info] iteration = 500 | max rel diff. = 0.653876
[2023-09-16 15:54:01.668] [jointLog] [info] iteration = 600 | max rel diff. = 6.36159
[2023-09-16 15:54:35.068] [jointLog] [info] iteration = 700 | max rel diff. = 0.111391
[2023-09-16 15:55:08.029] [jointLog] [info] iteration = 800 | max rel diff. = 0.350011
[2023-09-16 15:55:41.366] [jointLog] [info] iteration = 900 | max rel diff. = 5.89574
[2023-09-16 15:55:59.620] [jointLog] [info] iteration = 957 | max rel diff. = 0.0079278
[2023-09-16 15:56:01.674] [jointLog] [info] Finished optimizer
[2023-09-16 15:56:01.674] [jointLog] [info] writing output