[2023-09-28 06:28:07.714] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 06:28:07.714] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 06:28:07.714] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 06:28:07.714] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 06:28:07.714] [jointLog] [info] parsing read library format
[2023-09-28 06:28:07.714] [jointLog] [info] There is 1 library.
[2023-09-28 06:28:07.715] [jointLog] [info] Loading pufferfish index
[2023-09-28 06:28:07.715] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 06:29:27.034] [jointLog] [info] done
[2023-09-28 06:29:27.162] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 06:30:00.687] [jointLog] [info] Number of decoys : 194
[2023-09-28 06:30:00.687] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 06:30:01.989] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 06:30:03.328] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 06:30:55.873] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-09-28 06:30:55.905] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-28 06:30:55.907] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-09-28 06:30:56.004] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-28 06:30:56.020] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-28 06:30:56.050] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-28 06:30:56.217] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-28 06:30:56.252] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-09-28 06:30:56.438] [jointLog] [info] Computed 86,555 rich equivalence classes for further processing
[2023-09-28 06:30:56.438] [jointLog] [info] Counted 2,433,917 total reads in the equivalence classes 
[2023-09-28 06:30:56.447] [jointLog] [info] Number of mappings discarded because of alignment score : 71,747,818
[2023-09-28 06:30:56.447] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 332,895
[2023-09-28 06:30:56.447] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 78,264
[2023-09-28 06:30:56.447] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 06:30:56.439] [fileLog] [info] 
At end of round 0
==================
Observed 3394154 total fragments (3394154 in most recent round)

[2023-09-28 06:30:57.552] [jointLog] [warning] Only 2433917 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-28 06:30:57.553] [jointLog] [info] Mapping rate = 71.7091%

[2023-09-28 06:30:57.553] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 06:30:57.553] [jointLog] [info] Starting optimizer
[2023-09-28 06:31:01.184] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 06:31:01.519] [jointLog] [info] iteration = 0 | max rel diff. = 51.4794
[2023-09-28 06:31:04.834] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 06:31:56.302] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 06:31:56.302] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 06:32:00.981] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 06:32:05.819] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 06:32:10.502] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 06:32:15.458] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 06:32:20.061] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 06:32:24.710] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 06:32:29.263] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 06:32:34.126] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 06:32:38.652] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 06:32:43.455] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 06:33:14.265] [jointLog] [info] iteration = 100 | max rel diff. = 9.49758
[2023-09-28 06:33:47.735] [jointLog] [info] iteration = 200 | max rel diff. = 1.61062
[2023-09-28 06:34:20.760] [jointLog] [info] iteration = 300 | max rel diff. = 0.2666
[2023-09-28 06:34:53.702] [jointLog] [info] iteration = 400 | max rel diff. = 10.4892
[2023-09-28 06:35:27.073] [jointLog] [info] iteration = 500 | max rel diff. = 0.200709
[2023-09-28 06:36:00.025] [jointLog] [info] iteration = 600 | max rel diff. = 0.294141
[2023-09-28 06:36:34.348] [jointLog] [info] iteration = 700 | max rel diff. = 0.0107334
[2023-09-28 06:37:06.621] [jointLog] [info] iteration = 800 | max rel diff. = 0.886158
[2023-09-28 06:37:38.397] [jointLog] [info] iteration = 900 | max rel diff. = 0.0349594
[2023-09-28 06:37:47.892] [jointLog] [info] iteration = 931 | max rel diff. = 0.00662352
[2023-09-28 06:37:50.014] [jointLog] [info] Finished optimizer
[2023-09-28 06:37:50.014] [jointLog] [info] writing output