[2023-09-21 23:54:22.896] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 23:54:22.896] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 23:54:22.896] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 23:54:22.896] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 23:54:22.896] [jointLog] [info] parsing read library format
[2023-09-21 23:54:22.896] [jointLog] [info] There is 1 library.
[2023-09-21 23:54:22.897] [jointLog] [info] Loading pufferfish index
[2023-09-21 23:54:22.897] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 23:55:44.746] [jointLog] [info] done
[2023-09-21 23:55:44.908] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 23:56:24.730] [jointLog] [info] Number of decoys : 194
[2023-09-21 23:56:24.730] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 23:56:26.524] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 23:56:27.288] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 23:57:25.361] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-21 23:57:25.384] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-21 23:57:25.386] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
[2023-09-21 23:57:25.521] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-21 23:57:25.581] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-21 23:57:25.588] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-21 23:57:25.661] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-21 23:57:25.771] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-09-21 23:57:25.957] [jointLog] [info] Computed 100,796 rich equivalence classes for further processing
[2023-09-21 23:57:25.957] [jointLog] [info] Counted 3,639,233 total reads in the equivalence classes 
[2023-09-21 23:57:25.965] [jointLog] [info] Number of mappings discarded because of alignment score : 64,547,883
[2023-09-21 23:57:25.965] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 369,676
[2023-09-21 23:57:25.965] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 122,200
[2023-09-21 23:57:25.965] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 23:57:25.958] [fileLog] [info] 
At end of round 0
==================
Observed 4766296 total fragments (4766296 in most recent round)

[2023-09-21 23:57:27.188] [jointLog] [warning] Only 3639233 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 23:57:27.188] [jointLog] [info] Mapping rate = 76.3535%

[2023-09-21 23:57:27.188] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 23:57:27.188] [jointLog] [info] Starting optimizer
[2023-09-21 23:57:31.833] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 23:57:32.168] [jointLog] [info] iteration = 0 | max rel diff. = 71.0069
[2023-09-21 23:57:35.496] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 23:58:41.602] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 23:58:41.602] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 23:58:47.633] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 23:58:54.001] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 23:59:00.166] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 23:59:06.607] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 23:59:12.599] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 23:59:18.952] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 23:59:24.882] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 23:59:31.099] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 23:59:37.135] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 23:59:43.401] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-22 00:00:14.041] [jointLog] [info] iteration = 100 | max rel diff. = 19.8386
[2023-09-22 00:00:49.302] [jointLog] [info] iteration = 200 | max rel diff. = 1.16583
[2023-09-22 00:01:24.265] [jointLog] [info] iteration = 300 | max rel diff. = 0.243487
[2023-09-22 00:02:00.358] [jointLog] [info] iteration = 400 | max rel diff. = 2.93084
[2023-09-22 00:02:33.033] [jointLog] [info] iteration = 500 | max rel diff. = 0.0439445
[2023-09-22 00:03:05.434] [jointLog] [info] iteration = 600 | max rel diff. = 1.3028
[2023-09-22 00:03:38.059] [jointLog] [info] iteration = 700 | max rel diff. = 0.231298
[2023-09-22 00:04:09.976] [jointLog] [info] iteration = 800 | max rel diff. = 0.0106677
[2023-09-22 00:04:40.762] [jointLog] [info] iteration = 897 | max rel diff. = 0.0037285
[2023-09-22 00:04:43.157] [jointLog] [info] Finished optimizer
[2023-09-22 00:04:43.157] [jointLog] [info] writing output