[2023-10-04 18:36:27.538] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 18:36:27.538] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 18:36:27.539] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 18:36:27.539] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 18:36:27.539] [jointLog] [info] parsing read library format
[2023-10-04 18:36:27.539] [jointLog] [info] There is 1 library.
[2023-10-04 18:36:27.539] [jointLog] [info] Loading pufferfish index
[2023-10-04 18:36:27.539] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 18:37:58.050] [jointLog] [info] done
[2023-10-04 18:37:58.220] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 18:38:44.090] [jointLog] [info] Number of decoys : 194
[2023-10-04 18:38:44.090] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 18:38:46.565] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 18:38:47.370] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 18:39:45.251] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2023-10-04 18:39:45.292] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 18:39:45.327] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-04 18:39:45.446] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-04 18:39:45.492] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 18:39:45.565] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 18:39:45.601] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-04 18:39:45.676] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 18:39:45.907] [fileLog] [info] 
At end of round 0
==================
Observed 5038449 total fragments (5038449 in most recent round)

[2023-10-04 18:39:45.906] [jointLog] [info] Computed 86,325 rich equivalence classes for further processing
[2023-10-04 18:39:45.906] [jointLog] [info] Counted 3,615,587 total reads in the equivalence classes 
[2023-10-04 18:39:45.923] [jointLog] [info] Number of mappings discarded because of alignment score : 54,559,169
[2023-10-04 18:39:45.923] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 355,486
[2023-10-04 18:39:45.923] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 106,602
[2023-10-04 18:39:45.923] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 18:39:47.320] [jointLog] [warning] Only 3615587 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 18:39:47.320] [jointLog] [info] Mapping rate = 71.7599%

[2023-10-04 18:39:47.320] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 18:39:47.321] [jointLog] [info] Starting optimizer
[2023-10-04 18:39:53.410] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 18:39:53.815] [jointLog] [info] iteration = 0 | max rel diff. = 66.5465
[2023-10-04 18:39:57.572] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 18:41:03.366] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 18:41:03.366] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 18:41:09.060] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 18:41:14.847] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 18:41:21.923] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 18:41:28.298] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 18:41:34.223] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 18:41:40.816] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 18:41:48.922] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 18:41:56.282] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 18:42:01.928] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 18:42:08.957] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 18:42:43.076] [jointLog] [info] iteration = 100 | max rel diff. = 18.7728
[2023-10-04 18:43:19.132] [jointLog] [info] iteration = 200 | max rel diff. = 1.25989
[2023-10-04 18:43:55.262] [jointLog] [info] iteration = 300 | max rel diff. = 2.10666
[2023-10-04 18:44:29.533] [jointLog] [info] iteration = 400 | max rel diff. = 0.514314
[2023-10-04 18:45:04.763] [jointLog] [info] iteration = 500 | max rel diff. = 0.0248435
[2023-10-04 18:45:39.288] [jointLog] [info] iteration = 600 | max rel diff. = 0.016576
[2023-10-04 18:46:12.862] [jointLog] [info] iteration = 700 | max rel diff. = 0.0279109
[2023-10-04 18:46:46.574] [jointLog] [info] iteration = 800 | max rel diff. = 0.22697
[2023-10-04 18:47:19.462] [jointLog] [info] iteration = 900 | max rel diff. = 0.0154124
[2023-10-04 18:47:52.524] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.262707
[2023-10-04 18:47:56.521] [jointLog] [info] iteration = 1,013 | max rel diff. = 0.00666483
[2023-10-04 18:47:58.646] [jointLog] [info] Finished optimizer
[2023-10-04 18:47:58.646] [jointLog] [info] writing output