[2023-09-25 02:55:15.862] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 02:55:15.862] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 02:55:15.862] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 02:55:15.862] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 02:55:15.862] [jointLog] [info] parsing read library format
[2023-09-25 02:55:15.862] [jointLog] [info] There is 1 library.
[2023-09-25 02:55:15.862] [jointLog] [info] Loading pufferfish index
[2023-09-25 02:55:15.862] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 02:56:32.453] [jointLog] [info] done
[2023-09-25 02:56:32.576] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 02:57:08.058] [jointLog] [info] Number of decoys : 194
[2023-09-25 02:57:08.058] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 02:57:09.611] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 02:57:10.767] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 02:57:55.088] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-25 02:57:55.109] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-25 02:57:55.237] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-25 02:57:55.365] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-25 02:57:55.367] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-25 02:57:55.374] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-25 02:57:55.431] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-25 02:57:55.826] [fileLog] [info] 
At end of round 0
==================
Observed 3071546 total fragments (3071546 in most recent round)

[2023-09-25 02:57:55.661] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-25 02:57:55.825] [jointLog] [info] Computed 82,338 rich equivalence classes for further processing
[2023-09-25 02:57:55.825] [jointLog] [info] Counted 2,346,539 total reads in the equivalence classes 
[2023-09-25 02:57:55.833] [jointLog] [info] Number of mappings discarded because of alignment score : 58,749,879
[2023-09-25 02:57:55.833] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 308,961
[2023-09-25 02:57:55.833] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 80,514
[2023-09-25 02:57:55.833] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 02:57:56.672] [jointLog] [warning] Only 2346539 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-25 02:57:56.672] [jointLog] [info] Mapping rate = 76.396%

[2023-09-25 02:57:56.672] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 02:57:56.673] [jointLog] [info] Starting optimizer
[2023-09-25 02:58:00.346] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 02:58:00.676] [jointLog] [info] iteration = 0 | max rel diff. = 43.6939
[2023-09-25 02:58:03.941] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 02:58:56.102] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 02:58:56.102] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 02:59:00.493] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 02:59:05.089] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 02:59:09.941] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 02:59:14.900] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 02:59:19.326] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 02:59:24.272] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 02:59:29.187] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 02:59:33.994] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 02:59:38.618] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 02:59:43.589] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 03:00:13.095] [jointLog] [info] iteration = 100 | max rel diff. = 4.55963
[2023-09-25 03:00:45.525] [jointLog] [info] iteration = 200 | max rel diff. = 1.70856
[2023-09-25 03:01:17.835] [jointLog] [info] iteration = 300 | max rel diff. = 0.523033
[2023-09-25 03:01:50.091] [jointLog] [info] iteration = 400 | max rel diff. = 0.167853
[2023-09-25 03:02:22.400] [jointLog] [info] iteration = 500 | max rel diff. = 0.102385
[2023-09-25 03:02:54.478] [jointLog] [info] iteration = 600 | max rel diff. = 0.019652
[2023-09-25 03:03:18.222] [jointLog] [info] iteration = 674 | max rel diff. = 0.00617986
[2023-09-25 03:03:20.012] [jointLog] [info] Finished optimizer
[2023-09-25 03:03:20.012] [jointLog] [info] writing output