[2023-09-26 15:17:47.022] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 15:17:47.022] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 15:17:47.022] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 15:17:47.022] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 15:17:47.022] [jointLog] [info] parsing read library format
[2023-09-26 15:17:47.022] [jointLog] [info] There is 1 library.
[2023-09-26 15:17:47.022] [jointLog] [info] Loading pufferfish index
[2023-09-26 15:17:47.022] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 15:19:05.550] [jointLog] [info] done
[2023-09-26 15:19:05.671] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 15:19:42.996] [jointLog] [info] Number of decoys : 194
[2023-09-26 15:19:42.996] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 15:19:44.563] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 15:19:45.510] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 15:20:31.370] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-26 15:20:31.378] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-26 15:20:31.428] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-26 15:20:31.440] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-26 15:20:31.684] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-26 15:20:31.733] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-26 15:20:31.753] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-26 15:20:31.759] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-26 15:20:31.916] [jointLog] [info] Computed 89,990 rich equivalence classes for further processing
[2023-09-26 15:20:31.916] [jointLog] [info] Counted 1,861,108 total reads in the equivalence classes 
[2023-09-26 15:20:31.923] [jointLog] [warning] 0.00015885% 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 15:20:31.923] [jointLog] [info] Number of mappings discarded because of alignment score : 58,683,027
[2023-09-26 15:20:31.923] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 273,418
[2023-09-26 15:20:31.923] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 62,372
[2023-09-26 15:20:31.923] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 15:20:31.917] [fileLog] [info] 
At end of round 0
==================
Observed 2518098 total fragments (2518098 in most recent round)

[2023-09-26 15:20:32.842] [jointLog] [warning] Only 1861108 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 15:20:32.842] [jointLog] [info] Mapping rate = 73.9093%

[2023-09-26 15:20:32.842] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 15:20:32.844] [jointLog] [info] Starting optimizer
[2023-09-26 15:20:37.029] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 15:20:37.353] [jointLog] [info] iteration = 0 | max rel diff. = 36.9738
[2023-09-26 15:20:40.646] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 15:21:40.655] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 15:21:40.655] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 15:21:45.841] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 15:21:51.204] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 15:21:56.770] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 15:22:02.811] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 15:22:08.673] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 15:22:14.581] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 15:22:19.881] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 15:22:25.391] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 15:22:30.895] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 15:22:36.439] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 15:23:07.074] [jointLog] [info] iteration = 100 | max rel diff. = 2.07634
[2023-09-26 15:23:40.423] [jointLog] [info] iteration = 200 | max rel diff. = 1.2269
[2023-09-26 15:24:13.395] [jointLog] [info] iteration = 300 | max rel diff. = 5.49253
[2023-09-26 15:24:47.037] [jointLog] [info] iteration = 400 | max rel diff. = 0.182302
[2023-09-26 15:25:20.147] [jointLog] [info] iteration = 500 | max rel diff. = 0.0159884
[2023-09-26 15:25:52.600] [jointLog] [info] iteration = 600 | max rel diff. = 0.0385937
[2023-09-26 15:26:02.105] [jointLog] [info] iteration = 630 | max rel diff. = 0.00864821
[2023-09-26 15:26:04.359] [jointLog] [info] Finished optimizer
[2023-09-26 15:26:04.359] [jointLog] [info] writing output