[2023-09-25 06:16:47.026] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 06:16:47.026] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 06:16:47.026] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 06:16:47.026] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 06:16:47.026] [jointLog] [info] parsing read library format
[2023-09-25 06:16:47.027] [jointLog] [info] There is 1 library.
[2023-09-25 06:16:47.027] [jointLog] [info] Loading pufferfish index
[2023-09-25 06:16:47.027] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 06:18:01.940] [jointLog] [info] done
[2023-09-25 06:18:02.066] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 06:18:40.461] [jointLog] [info] Number of decoys : 194
[2023-09-25 06:18:40.461] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 06:18:42.285] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 06:18:43.084] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 06:19:27.301] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-25 06:19:27.316] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-25 06:19:27.423] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-25 06:19:27.455] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-09-25 06:19:27.504] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-25 06:19:27.547] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-25 06:19:27.572] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-25 06:19:28.006] [fileLog] [info] 
At end of round 0
==================
Observed 3672915 total fragments (3672915 in most recent round)

[2023-09-25 06:19:27.862] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-25 06:19:28.005] [jointLog] [info] Computed 84,823 rich equivalence classes for further processing
[2023-09-25 06:19:28.005] [jointLog] [info] Counted 2,723,219 total reads in the equivalence classes 
[2023-09-25 06:19:28.013] [jointLog] [info] Number of mappings discarded because of alignment score : 49,674,483
[2023-09-25 06:19:28.013] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 282,661
[2023-09-25 06:19:28.013] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 89,078
[2023-09-25 06:19:28.013] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 06:19:29.151] [jointLog] [warning] Only 2723219 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 06:19:29.151] [jointLog] [info] Mapping rate = 74.1433%

[2023-09-25 06:19:29.151] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 06:19:29.152] [jointLog] [info] Starting optimizer
[2023-09-25 06:19:33.737] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 06:19:34.071] [jointLog] [info] iteration = 0 | max rel diff. = 57.5194
[2023-09-25 06:19:37.435] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 06:20:32.364] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 06:20:32.364] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 06:20:37.007] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 06:20:41.961] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 06:20:47.085] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 06:20:52.543] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 06:20:57.570] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 06:21:02.671] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 06:21:07.693] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 06:21:12.462] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 06:21:17.816] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 06:21:23.170] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 06:21:23.258] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 06:21:53.835] [jointLog] [info] iteration = 100 | max rel diff. = 15.5197
[2023-09-25 06:22:26.984] [jointLog] [info] iteration = 200 | max rel diff. = 1.87431
[2023-09-25 06:23:00.345] [jointLog] [info] iteration = 300 | max rel diff. = 0.294478
[2023-09-25 06:23:33.516] [jointLog] [info] iteration = 400 | max rel diff. = 0.0685616
[2023-09-25 06:24:06.713] [jointLog] [info] iteration = 500 | max rel diff. = 0.0614724
[2023-09-25 06:24:39.895] [jointLog] [info] iteration = 600 | max rel diff. = 0.0329764
[2023-09-25 06:25:13.051] [jointLog] [info] iteration = 700 | max rel diff. = 0.126959
[2023-09-25 06:25:46.314] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123328
[2023-09-25 06:26:19.700] [jointLog] [info] iteration = 900 | max rel diff. = 0.257495
[2023-09-25 06:26:53.067] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.62425
[2023-09-25 06:27:16.004] [jointLog] [info] iteration = 1,070 | max rel diff. = 0.00144058
[2023-09-25 06:27:18.051] [jointLog] [info] Finished optimizer
[2023-09-25 06:27:18.051] [jointLog] [info] writing output