[2023-08-25 09:20:41.360] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 09:20:41.360] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 09:20:41.360] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 09:20:41.360] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 09:20:41.360] [jointLog] [info] parsing read library format
[2023-08-25 09:20:41.360] [jointLog] [info] There is 1 library.
[2023-08-25 09:20:41.360] [jointLog] [info] Loading pufferfish index
[2023-08-25 09:20:41.360] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 09:21:56.820] [jointLog] [info] done
[2023-08-25 09:21:56.939] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 09:22:33.068] [jointLog] [info] Number of decoys : 194
[2023-08-25 09:22:33.068] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 09:22:35.088] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 09:22:35.709] [jointLog] [info] Automatically detected most likely library type as SR

[2023-08-25 09:27:07.744] [jointLog] [info] Thread saw mini-batch with a maximum of 4.42% zero probability fragments
[2023-08-25 09:27:07.780] [jointLog] [info] Thread saw mini-batch with a maximum of 4.24% zero probability fragments
[2023-08-25 09:27:07.820] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
[2023-08-25 09:27:07.840] [jointLog] [info] Thread saw mini-batch with a maximum of 4.24% zero probability fragments
[2023-08-25 09:27:07.872] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
[2023-08-25 09:27:07.899] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-08-25 09:27:07.910] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
[2023-08-25 09:27:07.915] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments
[2023-08-25 09:27:08.524] [fileLog] [info] 
At end of round 0
==================
Observed 40014441 total fragments (40014441 in most recent round)

[2023-08-25 09:27:08.523] [jointLog] [info] Computed 448,089 rich equivalence classes for further processing
[2023-08-25 09:27:08.523] [jointLog] [info] Counted 37,206,041 total reads in the equivalence classes 
[2023-08-25 09:27:08.534] [jointLog] [warning] 0.0190881% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 30.


[2023-08-25 09:27:08.534] [jointLog] [info] Number of mappings discarded because of alignment score : 39,573,127
[2023-08-25 09:27:08.534] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 578,858
[2023-08-25 09:27:08.534] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 416,095
[2023-08-25 09:27:08.534] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 09:27:08.534] [jointLog] [info] Mapping rate = 92.9815%

[2023-08-25 09:27:08.534] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 09:27:08.536] [jointLog] [info] Starting optimizer
[2023-08-25 09:27:13.485] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 09:27:13.843] [jointLog] [info] iteration = 0 | max rel diff. = 446.989
[2023-08-25 09:27:17.429] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 09:29:27.806] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 09:29:27.806] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 09:29:39.520] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 09:29:51.533] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 09:30:03.958] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 09:30:16.279] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 09:30:28.122] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 09:30:40.187] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 09:30:52.147] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 09:31:04.249] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 09:31:16.166] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 09:31:28.140] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 09:32:00.634] [jointLog] [info] iteration = 100 | max rel diff. = 13.5306
[2023-08-25 09:32:37.035] [jointLog] [info] iteration = 200 | max rel diff. = 8.16816
[2023-08-25 09:33:13.377] [jointLog] [info] iteration = 300 | max rel diff. = 14.0754
[2023-08-25 09:33:48.592] [jointLog] [info] iteration = 400 | max rel diff. = 1.00065
[2023-08-25 09:34:23.246] [jointLog] [info] iteration = 500 | max rel diff. = 2.19896
[2023-08-25 09:34:58.107] [jointLog] [info] iteration = 600 | max rel diff. = 0.888443
[2023-08-25 09:35:33.188] [jointLog] [info] iteration = 700 | max rel diff. = 3.99377
[2023-08-25 09:36:07.991] [jointLog] [info] iteration = 800 | max rel diff. = 0.253002
[2023-08-25 09:36:42.860] [jointLog] [info] iteration = 900 | max rel diff. = 0.112074
[2023-08-25 09:37:17.394] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.383039
[2023-08-25 09:37:53.971] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.332411
[2023-08-25 09:38:30.224] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0602343
[2023-08-25 09:39:06.606] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.14265
[2023-08-25 09:39:42.888] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.224033
[2023-08-25 09:40:19.380] [jointLog] [info] iteration = 1,500 | max rel diff. = 13.8593
[2023-08-25 09:40:54.431] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.213466
[2023-08-25 09:41:29.398] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.265461
[2023-08-25 09:42:03.872] [jointLog] [info] iteration = 1,800 | max rel diff. = 0.0687169
[2023-08-25 09:42:38.431] [jointLog] [info] iteration = 1,900 | max rel diff. = 0.0432489
[2023-08-25 09:43:13.613] [jointLog] [info] iteration = 2,000 | max rel diff. = 0.0676588
[2023-08-25 09:43:22.294] [jointLog] [info] iteration = 2,026 | max rel diff. = 0.0074251
[2023-08-25 09:43:24.149] [jointLog] [info] Finished optimizer
[2023-08-25 09:43:24.149] [jointLog] [info] writing output