[2023-09-21 03:13:40.675] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 03:13:40.675] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 03:13:40.675] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 03:13:40.675] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 03:13:40.675] [jointLog] [info] parsing read library format
[2023-09-21 03:13:40.675] [jointLog] [info] There is 1 library.
[2023-09-21 03:13:40.675] [jointLog] [info] Loading pufferfish index
[2023-09-21 03:13:40.675] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 03:14:53.109] [jointLog] [info] done
[2023-09-21 03:14:53.292] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 03:15:34.918] [jointLog] [info] Number of decoys : 194
[2023-09-21 03:15:34.918] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 03:15:37.591] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 03:15:38.637] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 03:16:21.460] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-21 03:16:21.617] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-21 03:16:21.662] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-09-21 03:16:21.711] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-21 03:16:21.717] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-09-21 03:16:21.744] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-21 03:16:21.777] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-09-21 03:16:21.975] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-21 03:16:22.220] [fileLog] [info] 
At end of round 0
==================
Observed 2909885 total fragments (2909885 in most recent round)

[2023-09-21 03:16:22.219] [jointLog] [info] Computed 81,726 rich equivalence classes for further processing
[2023-09-21 03:16:22.219] [jointLog] [info] Counted 2,039,933 total reads in the equivalence classes 
[2023-09-21 03:16:22.227] [jointLog] [info] Number of mappings discarded because of alignment score : 56,586,134
[2023-09-21 03:16:22.227] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 338,841
[2023-09-21 03:16:22.227] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 60,895
[2023-09-21 03:16:22.227] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 03:16:23.843] [jointLog] [warning] Only 2039933 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 03:16:23.843] [jointLog] [info] Mapping rate = 70.1036%

[2023-09-21 03:16:23.843] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 03:16:23.843] [jointLog] [info] Starting optimizer
[2023-09-21 03:16:29.275] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 03:16:29.613] [jointLog] [info] iteration = 0 | max rel diff. = 39.0058
[2023-09-21 03:16:33.079] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 03:17:25.714] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 03:17:25.715] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 03:17:30.391] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 03:17:35.496] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 03:17:40.177] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 03:17:45.205] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 03:17:49.956] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 03:17:54.786] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 03:17:59.295] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 03:18:04.319] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 03:18:09.158] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 03:18:14.206] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 03:18:47.319] [jointLog] [info] iteration = 100 | max rel diff. = 10.4244
[2023-09-21 03:19:22.459] [jointLog] [info] iteration = 200 | max rel diff. = 5.50414
[2023-09-21 03:19:57.313] [jointLog] [info] iteration = 300 | max rel diff. = 0.462107
[2023-09-21 03:20:32.009] [jointLog] [info] iteration = 400 | max rel diff. = 0.491691
[2023-09-21 03:21:06.833] [jointLog] [info] iteration = 500 | max rel diff. = 0.713469
[2023-09-21 03:21:41.080] [jointLog] [info] iteration = 600 | max rel diff. = 0.111459
[2023-09-21 03:21:49.304] [jointLog] [info] iteration = 625 | max rel diff. = 0.00426359
[2023-09-21 03:21:51.893] [jointLog] [info] Finished optimizer
[2023-09-21 03:21:51.894] [jointLog] [info] writing output