[2023-09-26 14:20:14.328] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 14:20:14.328] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 14:20:14.328] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 14:20:14.328] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 14:20:14.328] [jointLog] [info] parsing read library format
[2023-09-26 14:20:14.328] [jointLog] [info] There is 1 library.
[2023-09-26 14:20:14.329] [jointLog] [info] Loading pufferfish index
[2023-09-26 14:20:14.329] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 14:21:30.712] [jointLog] [info] done
[2023-09-26 14:21:30.844] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 14:22:10.194] [jointLog] [info] Number of decoys : 194
[2023-09-26 14:22:10.194] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 14:22:12.275] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 14:22:13.015] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 14:22:39.152] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-26 14:22:39.292] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-26 14:22:39.357] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-26 14:22:39.429] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-26 14:22:39.466] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-26 14:22:39.481] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-26 14:22:39.536] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-26 14:22:39.588] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-26 14:22:39.772] [jointLog] [info] Computed 78,029 rich equivalence classes for further processing
[2023-09-26 14:22:39.772] [jointLog] [info] Counted 1,332,740 total reads in the equivalence classes 
[2023-09-26 14:22:39.783] [jointLog] [warning] 0.000108544% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 10.


[2023-09-26 14:22:39.783] [jointLog] [info] Number of mappings discarded because of alignment score : 30,341,312
[2023-09-26 14:22:39.783] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 182,464
[2023-09-26 14:22:39.783] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 48,197
[2023-09-26 14:22:39.783] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 14:22:39.773] [fileLog] [info] 
At end of round 0
==================
Observed 1842564 total fragments (1842564 in most recent round)

[2023-09-26 14:22:41.352] [jointLog] [warning] Only 1332740 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 14:22:41.352] [jointLog] [info] Mapping rate = 72.3307%

[2023-09-26 14:22:41.352] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 14:22:41.353] [jointLog] [info] Starting optimizer
[2023-09-26 14:22:46.359] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 14:22:46.704] [jointLog] [info] iteration = 0 | max rel diff. = 25.0979
[2023-09-26 14:22:50.258] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 14:23:43.888] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 14:23:43.889] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 14:23:48.747] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 14:23:53.554] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 14:23:58.533] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 14:24:03.650] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 14:24:08.293] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 14:24:13.564] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 14:24:18.670] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 14:24:23.698] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 14:24:28.524] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 14:24:33.533] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 14:25:04.984] [jointLog] [info] iteration = 100 | max rel diff. = 9.13321
[2023-09-26 14:25:39.869] [jointLog] [info] iteration = 200 | max rel diff. = 7.75727
[2023-09-26 14:26:14.523] [jointLog] [info] iteration = 300 | max rel diff. = 0.909981
[2023-09-26 14:26:49.081] [jointLog] [info] iteration = 400 | max rel diff. = 0.15208
[2023-09-26 14:27:22.970] [jointLog] [info] iteration = 500 | max rel diff. = 0.071126
[2023-09-26 14:27:57.550] [jointLog] [info] iteration = 600 | max rel diff. = 0.0840511
[2023-09-26 14:28:02.739] [jointLog] [info] iteration = 616 | max rel diff. = 0.00872293
[2023-09-26 14:28:04.996] [jointLog] [info] Finished optimizer
[2023-09-26 14:28:04.996] [jointLog] [info] writing output