[2023-09-20 14:24:32.305] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 14:24:32.305] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 14:24:32.305] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 14:24:32.305] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 14:24:32.305] [jointLog] [info] parsing read library format
[2023-09-20 14:24:32.306] [jointLog] [info] There is 1 library.
[2023-09-20 14:24:32.306] [jointLog] [info] Loading pufferfish index
[2023-09-20 14:24:32.306] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 14:25:44.085] [jointLog] [info] done
[2023-09-20 14:25:44.203] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 14:26:19.585] [jointLog] [info] Number of decoys : 194
[2023-09-20 14:26:19.585] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 14:26:21.302] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 14:26:22.290] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 14:26:58.745] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-20 14:26:58.749] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-20 14:26:58.782] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-20 14:26:58.836] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-20 14:26:58.894] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-20 14:26:59.027] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-20 14:26:59.041] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-09-20 14:26:59.059] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-09-20 14:26:59.208] [jointLog] [info] Computed 87,059 rich equivalence classes for further processing
[2023-09-20 14:26:59.208] [jointLog] [info] Counted 2,436,842 total reads in the equivalence classes 
[2023-09-20 14:26:59.215] [jointLog] [info] Number of mappings discarded because of alignment score : 37,430,644
[2023-09-20 14:26:59.215] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 302,780
[2023-09-20 14:26:59.215] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 62,068
[2023-09-20 14:26:59.215] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 14:26:59.209] [fileLog] [info] 
At end of round 0
==================
Observed 3144404 total fragments (3144404 in most recent round)

[2023-09-20 14:27:00.090] [jointLog] [warning] Only 2436842 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 14:27:00.090] [jointLog] [info] Mapping rate = 77.4977%

[2023-09-20 14:27:00.090] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 14:27:00.091] [jointLog] [info] Starting optimizer
[2023-09-20 14:27:04.140] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 14:27:04.466] [jointLog] [info] iteration = 0 | max rel diff. = 52.2173
[2023-09-20 14:27:07.717] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 14:27:59.418] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 14:27:59.419] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 14:28:03.985] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 14:28:08.763] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 14:28:13.343] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 14:28:18.252] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 14:28:22.747] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 14:28:27.822] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 14:28:32.512] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 14:28:37.241] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 14:28:42.282] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 14:28:46.954] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 14:29:15.956] [jointLog] [info] iteration = 100 | max rel diff. = 11.5854
[2023-09-20 14:29:48.107] [jointLog] [info] iteration = 200 | max rel diff. = 1.80401
[2023-09-20 14:30:20.424] [jointLog] [info] iteration = 300 | max rel diff. = 1.99175
[2023-09-20 14:30:52.830] [jointLog] [info] iteration = 400 | max rel diff. = 0.138879
[2023-09-20 14:31:25.356] [jointLog] [info] iteration = 500 | max rel diff. = 0.0315891
[2023-09-20 14:31:57.866] [jointLog] [info] iteration = 600 | max rel diff. = 0.417578
[2023-09-20 14:32:30.181] [jointLog] [info] iteration = 700 | max rel diff. = 0.0202773
[2023-09-20 14:33:02.651] [jointLog] [info] iteration = 800 | max rel diff. = 0.0285907
[2023-09-20 14:33:29.721] [jointLog] [info] iteration = 884 | max rel diff. = 0.00588912
[2023-09-20 14:33:31.709] [jointLog] [info] Finished optimizer
[2023-09-20 14:33:31.709] [jointLog] [info] writing output