[2023-09-16 00:17:13.927] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 00:17:13.927] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 00:17:13.927] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 00:17:13.927] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 00:17:13.927] [jointLog] [info] parsing read library format
[2023-09-16 00:17:13.927] [jointLog] [info] There is 1 library.
[2023-09-16 00:17:13.927] [jointLog] [info] Loading pufferfish index
[2023-09-16 00:17:13.927] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 00:18:28.704] [jointLog] [info] done
[2023-09-16 00:18:28.884] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 00:19:07.951] [jointLog] [info] Number of decoys : 194
[2023-09-16 00:19:07.951] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 00:19:09.670] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 00:19:10.203] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 00:19:47.269] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments
[2023-09-16 00:19:47.287] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2023-09-16 00:19:47.346] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-09-16 00:19:47.377] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-09-16 00:19:47.424] [jointLog] [info] Thread saw mini-batch with a maximum of 4.34% zero probability fragments
[2023-09-16 00:19:47.426] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-09-16 00:19:47.431] [jointLog] [info] Thread saw mini-batch with a maximum of 4.14% zero probability fragments
[2023-09-16 00:19:47.456] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments
[2023-09-16 00:19:47.722] [fileLog] [info] 
At end of round 0
==================
Observed 6223369 total fragments (6223369 in most recent round)

[2023-09-16 00:19:47.721] [jointLog] [info] Computed 203,321 rich equivalence classes for further processing
[2023-09-16 00:19:47.721] [jointLog] [info] Counted 5,684,894 total reads in the equivalence classes 
[2023-09-16 00:19:47.732] [jointLog] [info] Number of mappings discarded because of alignment score : 8,813,249
[2023-09-16 00:19:47.732] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 56,784
[2023-09-16 00:19:47.732] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 39,244
[2023-09-16 00:19:47.732] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 00:19:47.732] [jointLog] [info] Mapping rate = 91.3475%

[2023-09-16 00:19:47.732] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 00:19:47.732] [jointLog] [info] Starting optimizer
[2023-09-16 00:19:52.685] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 00:19:53.041] [jointLog] [info] iteration = 0 | max rel diff. = 133.795
[2023-09-16 00:19:56.513] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 00:21:05.798] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 00:21:05.799] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 00:21:12.257] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 00:21:18.639] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 00:21:25.178] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 00:21:31.656] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 00:21:37.979] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 00:21:44.130] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 00:21:50.407] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 00:21:56.824] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 00:22:02.994] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 00:22:09.703] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 00:22:40.981] [jointLog] [info] iteration = 100 | max rel diff. = 11.6952
[2023-09-16 00:23:15.509] [jointLog] [info] iteration = 200 | max rel diff. = 10.487
[2023-09-16 00:23:49.353] [jointLog] [info] iteration = 300 | max rel diff. = 7.58927
[2023-09-16 00:24:22.999] [jointLog] [info] iteration = 400 | max rel diff. = 11.8293
[2023-09-16 00:24:57.444] [jointLog] [info] iteration = 500 | max rel diff. = 0.816074
[2023-09-16 00:25:31.124] [jointLog] [info] iteration = 600 | max rel diff. = 0.397114
[2023-09-16 00:26:05.373] [jointLog] [info] iteration = 700 | max rel diff. = 0.271052
[2023-09-16 00:26:38.279] [jointLog] [info] iteration = 800 | max rel diff. = 0.106133
[2023-09-16 00:27:10.837] [jointLog] [info] iteration = 900 | max rel diff. = 0.153324
[2023-09-16 00:27:43.516] [jointLog] [info] iteration = 1,000 | max rel diff. = 6.70222
[2023-09-16 00:28:16.514] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.048959
[2023-09-16 00:28:46.149] [jointLog] [info] iteration = 1,192 | max rel diff. = 0.0050611
[2023-09-16 00:28:48.061] [jointLog] [info] Finished optimizer
[2023-09-16 00:28:48.061] [jointLog] [info] writing output