[2023-10-04 16:33:40.362] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 16:33:40.362] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 16:33:40.362] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 16:33:40.362] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 16:33:40.362] [jointLog] [info] parsing read library format
[2023-10-04 16:33:40.362] [jointLog] [info] There is 1 library.
[2023-10-04 16:33:40.362] [jointLog] [info] Loading pufferfish index
[2023-10-04 16:33:40.362] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 16:35:04.965] [jointLog] [info] done
[2023-10-04 16:35:05.103] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 16:35:42.405] [jointLog] [info] Number of decoys : 194
[2023-10-04 16:35:42.405] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 16:35:43.949] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 16:35:44.730] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 16:36:30.140] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-04 16:36:30.255] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 16:36:30.277] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 16:36:30.376] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-04 16:36:30.394] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 16:36:30.474] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-04 16:36:30.483] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 16:36:30.633] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 16:36:30.780] [jointLog] [info] Computed 79,609 rich equivalence classes for further processing
[2023-10-04 16:36:30.780] [jointLog] [info] Counted 3,120,792 total reads in the equivalence classes 
[2023-10-04 16:36:30.787] [jointLog] [info] Number of mappings discarded because of alignment score : 51,683,027
[2023-10-04 16:36:30.787] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 332,990
[2023-10-04 16:36:30.787] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 100,679
[2023-10-04 16:36:30.787] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 16:36:30.781] [fileLog] [info] 
At end of round 0
==================
Observed 4139469 total fragments (4139469 in most recent round)

[2023-10-04 16:36:31.521] [jointLog] [warning] Only 3120792 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 16:36:31.521] [jointLog] [info] Mapping rate = 75.3911%

[2023-10-04 16:36:31.521] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 16:36:31.521] [jointLog] [info] Starting optimizer
[2023-10-04 16:36:34.999] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 16:36:35.331] [jointLog] [info] iteration = 0 | max rel diff. = 68.6712
[2023-10-04 16:36:38.775] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 16:37:30.027] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 16:37:30.028] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 16:37:35.945] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 16:37:43.732] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 16:37:48.426] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 16:37:54.155] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 16:37:58.586] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 16:38:03.458] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 16:38:07.948] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 16:38:17.020] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 16:38:24.048] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 16:38:29.019] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 16:38:57.790] [jointLog] [info] iteration = 100 | max rel diff. = 12.4652
[2023-10-04 16:39:30.067] [jointLog] [info] iteration = 200 | max rel diff. = 0.789552
[2023-10-04 16:40:02.142] [jointLog] [info] iteration = 300 | max rel diff. = 0.234502
[2023-10-04 16:40:34.457] [jointLog] [info] iteration = 400 | max rel diff. = 0.316004
[2023-10-04 16:41:06.734] [jointLog] [info] iteration = 500 | max rel diff. = 0.0461225
[2023-10-04 16:41:39.864] [jointLog] [info] iteration = 600 | max rel diff. = 0.0303313
[2023-10-04 16:42:11.953] [jointLog] [info] iteration = 700 | max rel diff. = 0.209326
[2023-10-04 16:42:43.403] [jointLog] [info] iteration = 800 | max rel diff. = 0.681183
[2023-10-04 16:43:15.804] [jointLog] [info] iteration = 900 | max rel diff. = 0.0297914
[2023-10-04 16:43:48.358] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.223983
[2023-10-04 16:44:21.492] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0387536
[2023-10-04 16:44:46.287] [jointLog] [info] iteration = 1,176 | max rel diff. = 0.000897237
[2023-10-04 16:44:48.162] [jointLog] [info] Finished optimizer
[2023-10-04 16:44:48.162] [jointLog] [info] writing output