[2023-08-25 03:56:22.108] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 03:56:22.108] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 03:56:22.108] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 03:56:22.108] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 03:56:22.108] [jointLog] [info] parsing read library format
[2023-08-25 03:56:22.108] [jointLog] [info] There is 1 library.
[2023-08-25 03:56:22.108] [jointLog] [info] Loading pufferfish index
[2023-08-25 03:56:22.108] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 04:03:24.533] [jointLog] [info] done
[2023-08-25 04:03:25.247] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 04:06:41.832] [jointLog] [info] Number of decoys : 194
[2023-08-25 04:06:41.832] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 04:06:50.739] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 04:06:58.171] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 04:27:34.315] [jointLog] [info] Thread saw mini-batch with a maximum of 6.14% zero probability fragments
[2023-08-25 04:27:34.623] [jointLog] [info] Thread saw mini-batch with a maximum of 6.14% zero probability fragments
[2023-08-25 04:27:34.692] [jointLog] [info] Thread saw mini-batch with a maximum of 6.18% zero probability fragments
[2023-08-25 04:27:34.882] [jointLog] [info] Thread saw mini-batch with a maximum of 6.18% zero probability fragments
[2023-08-25 04:27:35.064] [jointLog] [info] Thread saw mini-batch with a maximum of 6.16% zero probability fragments
[2023-08-25 04:27:35.074] [jointLog] [info] Thread saw mini-batch with a maximum of 6.10% zero probability fragments
[2023-08-25 04:27:35.077] [jointLog] [info] Thread saw mini-batch with a maximum of 6.12% zero probability fragments
[2023-08-25 04:27:35.945] [jointLog] [info] Thread saw mini-batch with a maximum of 6.02% zero probability fragments
[2023-08-25 04:27:37.375] [jointLog] [info] Computed 288,467 rich equivalence classes for further processing
[2023-08-25 04:27:37.375] [jointLog] [info] Counted 18,201,376 total reads in the equivalence classes 
[2023-08-25 04:27:37.404] [jointLog] [info] Number of mappings discarded because of alignment score : 33,796,335
[2023-08-25 04:27:37.404] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 484,651
[2023-08-25 04:27:37.404] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 226,098
[2023-08-25 04:27:37.404] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 04:27:37.404] [jointLog] [info] Mapping rate = 89.3207%

[2023-08-25 04:27:37.404] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 04:27:37.404] [jointLog] [info] Starting optimizer
[2023-08-25 04:27:37.376] [fileLog] [info] 
At end of round 0
==================
Observed 20377557 total fragments (20377557 in most recent round)

[2023-08-25 04:27:53.739] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 04:27:57.326] [jointLog] [info] iteration = 0 | max rel diff. = 242.081
[2023-08-25 04:28:21.836] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 04:36:48.360] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 04:36:48.362] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 04:37:49.566] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 04:38:46.775] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 04:39:42.720] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 04:40:40.677] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 04:41:36.888] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 04:42:31.733] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 04:43:31.272] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 04:44:32.516] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 04:45:31.754] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 04:46:34.516] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 04:46:34.516] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 04:50:29.016] [jointLog] [info] iteration = 100 | max rel diff. = 16.6135
[2023-08-25 04:54:33.278] [jointLog] [info] iteration = 200 | max rel diff. = 11.0153
[2023-08-25 04:59:00.179] [jointLog] [info] iteration = 300 | max rel diff. = 4.97858
[2023-08-25 05:03:21.129] [jointLog] [info] iteration = 400 | max rel diff. = 3.49703
[2023-08-25 05:07:43.029] [jointLog] [info] iteration = 500 | max rel diff. = 0.26124
[2023-08-25 05:12:16.724] [jointLog] [info] iteration = 600 | max rel diff. = 2.6121
[2023-08-25 05:16:30.925] [jointLog] [info] iteration = 700 | max rel diff. = 10.1687
[2023-08-25 05:20:36.763] [jointLog] [info] iteration = 800 | max rel diff. = 0.607155
[2023-08-25 05:24:52.870] [jointLog] [info] iteration = 900 | max rel diff. = 0.399749
[2023-08-25 05:29:19.512] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.032377
[2023-08-25 05:33:16.555] [jointLog] [info] iteration = 1,090 | max rel diff. = 0.00885401
[2023-08-25 05:33:25.167] [jointLog] [info] Finished optimizer
[2023-08-25 05:33:25.167] [jointLog] [info] writing output