[2023-10-04 18:14:38.791] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 18:14:38.791] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 18:14:38.791] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 18:14:38.791] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 18:14:38.791] [jointLog] [info] parsing read library format
[2023-10-04 18:14:38.791] [jointLog] [info] There is 1 library.
[2023-10-04 18:14:38.791] [jointLog] [info] Loading pufferfish index
[2023-10-04 18:14:38.791] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 18:15:59.968] [jointLog] [info] done
[2023-10-04 18:16:00.106] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 18:16:37.940] [jointLog] [info] Number of decoys : 194
[2023-10-04 18:16:37.940] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 18:16:39.843] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 18:16:40.985] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 18:17:31.084] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-04 18:17:31.111] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-04 18:17:31.115] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 18:17:31.116] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 18:17:31.205] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 18:17:31.321] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 18:17:31.410] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-10-04 18:17:31.519] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-04 18:17:31.681] [jointLog] [info] Computed 82,593 rich equivalence classes for further processing
[2023-10-04 18:17:31.681] [jointLog] [info] Counted 3,602,202 total reads in the equivalence classes 
[2023-10-04 18:17:31.688] [jointLog] [info] Number of mappings discarded because of alignment score : 48,229,528
[2023-10-04 18:17:31.688] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 365,044
[2023-10-04 18:17:31.688] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 123,518
[2023-10-04 18:17:31.688] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 18:17:31.682] [fileLog] [info] 
At end of round 0
==================
Observed 4721983 total fragments (4721983 in most recent round)

[2023-10-04 18:17:32.738] [jointLog] [warning] Only 3602202 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 18:17:32.738] [jointLog] [info] Mapping rate = 76.2858%

[2023-10-04 18:17:32.738] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 18:17:32.739] [jointLog] [info] Starting optimizer
[2023-10-04 18:17:36.547] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 18:17:36.889] [jointLog] [info] iteration = 0 | max rel diff. = 79.5772
[2023-10-04 18:17:40.235] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 18:18:34.230] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 18:18:34.231] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 18:18:39.252] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 18:18:44.290] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 18:18:49.099] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 18:18:54.090] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 18:18:58.865] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 18:19:03.807] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 18:19:08.688] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 18:19:13.540] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 18:19:18.351] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 18:19:23.072] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 18:19:23.072] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 18:19:52.715] [jointLog] [info] iteration = 100 | max rel diff. = 14.6074
[2023-10-04 18:20:26.691] [jointLog] [info] iteration = 200 | max rel diff. = 0.924797
[2023-10-04 18:20:59.376] [jointLog] [info] iteration = 300 | max rel diff. = 0.170237
[2023-10-04 18:21:31.198] [jointLog] [info] iteration = 400 | max rel diff. = 1.56538
[2023-10-04 18:22:03.396] [jointLog] [info] iteration = 500 | max rel diff. = 0.158238
[2023-10-04 18:22:36.015] [jointLog] [info] iteration = 600 | max rel diff. = 0.0386641
[2023-10-04 18:23:08.339] [jointLog] [info] iteration = 700 | max rel diff. = 0.0722219
[2023-10-04 18:23:40.478] [jointLog] [info] iteration = 800 | max rel diff. = 0.0133915
[2023-10-04 18:24:12.719] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120399
[2023-10-04 18:24:44.837] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0342471
[2023-10-04 18:24:58.642] [jointLog] [info] iteration = 1,044 | max rel diff. = 0.00322468
[2023-10-04 18:25:00.206] [jointLog] [info] Finished optimizer
[2023-10-04 18:25:00.206] [jointLog] [info] writing output