[2023-09-23 23:36:46.053] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 23:36:46.053] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 23:36:46.053] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 23:36:46.053] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 23:36:46.053] [jointLog] [info] parsing read library format
[2023-09-23 23:36:46.054] [jointLog] [info] There is 1 library.
[2023-09-23 23:36:46.054] [jointLog] [info] Loading pufferfish index
[2023-09-23 23:36:46.054] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 23:38:03.034] [jointLog] [info] done
[2023-09-23 23:38:03.186] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 23:38:42.591] [jointLog] [info] Number of decoys : 194
[2023-09-23 23:38:42.591] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 23:38:44.230] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 23:38:44.810] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 23:39:56.308] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-23 23:39:56.313] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-23 23:39:56.404] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-23 23:39:56.542] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-23 23:39:56.583] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-23 23:39:57.098] [fileLog] [info] 
At end of round 0
==================
Observed 5710673 total fragments (5710673 in most recent round)

[2023-09-23 23:39:56.808] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-09-23 23:39:56.846] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-23 23:39:56.898] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-23 23:39:57.097] [jointLog] [info] Computed 91,863 rich equivalence classes for further processing
[2023-09-23 23:39:57.097] [jointLog] [info] Counted 4,502,319 total reads in the equivalence classes 
[2023-09-23 23:39:57.106] [jointLog] [info] Number of mappings discarded because of alignment score : 90,072,803
[2023-09-23 23:39:57.106] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 550,678
[2023-09-23 23:39:57.106] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 135,276
[2023-09-23 23:39:57.106] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 23:39:58.496] [jointLog] [warning] Only 4502319 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 23:39:58.496] [jointLog] [info] Mapping rate = 78.8404%

[2023-09-23 23:39:58.496] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 23:39:58.496] [jointLog] [info] Starting optimizer
[2023-09-23 23:40:03.069] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 23:40:03.412] [jointLog] [info] iteration = 0 | max rel diff. = 129.305
[2023-09-23 23:40:06.810] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 23:41:02.246] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 23:41:02.247] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 23:41:07.351] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 23:41:12.330] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 23:41:17.081] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 23:41:22.373] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 23:41:27.334] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 23:41:32.501] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 23:41:37.626] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 23:41:42.388] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 23:41:47.125] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 23:41:52.533] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 23:42:23.593] [jointLog] [info] iteration = 100 | max rel diff. = 20.3711
[2023-09-23 23:42:57.497] [jointLog] [info] iteration = 200 | max rel diff. = 9.21366
[2023-09-23 23:43:30.800] [jointLog] [info] iteration = 300 | max rel diff. = 0.636348
[2023-09-23 23:44:04.507] [jointLog] [info] iteration = 400 | max rel diff. = 0.316337
[2023-09-23 23:44:38.040] [jointLog] [info] iteration = 500 | max rel diff. = 0.107844
[2023-09-23 23:45:11.227] [jointLog] [info] iteration = 600 | max rel diff. = 3.27779
[2023-09-23 23:45:44.520] [jointLog] [info] iteration = 700 | max rel diff. = 0.0347564
[2023-09-23 23:46:17.790] [jointLog] [info] iteration = 800 | max rel diff. = 0.0916422
[2023-09-23 23:46:51.447] [jointLog] [info] iteration = 900 | max rel diff. = 0.104037
[2023-09-23 23:47:24.700] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.107271
[2023-09-23 23:47:41.718] [jointLog] [info] iteration = 1,052 | max rel diff. = 0.0039839
[2023-09-23 23:47:43.773] [jointLog] [info] Finished optimizer
[2023-09-23 23:47:43.773] [jointLog] [info] writing output