[2023-09-24 08:17:50.556] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 08:17:50.556] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 08:17:50.556] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 08:17:50.556] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 08:17:50.556] [jointLog] [info] parsing read library format
[2023-09-24 08:17:50.556] [jointLog] [info] There is 1 library.
[2023-09-24 08:17:50.557] [jointLog] [info] Loading pufferfish index
[2023-09-24 08:17:50.557] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 08:19:03.300] [jointLog] [info] done
[2023-09-24 08:19:03.462] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 08:19:43.293] [jointLog] [info] Number of decoys : 194
[2023-09-24 08:19:43.293] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 08:19:45.948] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 08:19:46.779] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 08:20:24.948] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-09-24 08:20:25.076] [jointLog] [info] Thread saw mini-batch with a maximum of 4.38% zero probability fragments
[2023-09-24 08:20:25.196] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-09-24 08:20:25.234] [jointLog] [info] Thread saw mini-batch with a maximum of 4.38% zero probability fragments
[2023-09-24 08:20:25.281] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-09-24 08:20:25.303] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2023-09-24 08:20:25.441] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-24 08:20:25.447] [jointLog] [info] Thread saw mini-batch with a maximum of 4.28% zero probability fragments
[2023-09-24 08:20:25.641] [jointLog] [info] Computed 76,536 rich equivalence classes for further processing
[2023-09-24 08:20:25.641] [jointLog] [info] Counted 1,860,275 total reads in the equivalence classes 
[2023-09-24 08:20:25.648] [jointLog] [info] Number of mappings discarded because of alignment score : 48,816,922
[2023-09-24 08:20:25.648] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 248,809
[2023-09-24 08:20:25.648] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 64,230
[2023-09-24 08:20:25.648] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 08:20:25.642] [fileLog] [info] 
At end of round 0
==================
Observed 2444415 total fragments (2444415 in most recent round)

[2023-09-24 08:20:26.904] [jointLog] [warning] Only 1860275 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 08:20:26.904] [jointLog] [info] Mapping rate = 76.1031%

[2023-09-24 08:20:26.904] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 08:20:26.905] [jointLog] [info] Starting optimizer
[2023-09-24 08:20:31.571] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 08:20:31.911] [jointLog] [info] iteration = 0 | max rel diff. = 36.5712
[2023-09-24 08:20:35.252] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 08:21:26.789] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 08:21:26.790] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 08:21:31.407] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 08:21:35.954] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 08:21:40.777] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 08:21:45.725] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 08:21:50.692] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 08:21:55.569] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 08:22:00.071] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 08:22:04.805] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 08:22:09.511] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 08:22:14.054] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 08:22:44.242] [jointLog] [info] iteration = 100 | max rel diff. = 11.0923
[2023-09-24 08:23:17.672] [jointLog] [info] iteration = 200 | max rel diff. = 4.12269
[2023-09-24 08:23:49.578] [jointLog] [info] iteration = 300 | max rel diff. = 1.55437
[2023-09-24 08:24:21.100] [jointLog] [info] iteration = 400 | max rel diff. = 0.718153
[2023-09-24 08:24:52.435] [jointLog] [info] iteration = 500 | max rel diff. = 0.127967
[2023-09-24 08:25:24.541] [jointLog] [info] iteration = 600 | max rel diff. = 0.0544791
[2023-09-24 08:25:33.161] [jointLog] [info] iteration = 628 | max rel diff. = 0.00508732
[2023-09-24 08:25:35.218] [jointLog] [info] Finished optimizer
[2023-09-24 08:25:35.218] [jointLog] [info] writing output