[2023-10-05 09:20:40.583] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 09:20:40.583] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 09:20:40.583] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 09:20:40.583] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 09:20:40.583] [jointLog] [info] parsing read library format
[2023-10-05 09:20:40.583] [jointLog] [info] There is 1 library.
[2023-10-05 09:20:40.583] [jointLog] [info] Loading pufferfish index
[2023-10-05 09:20:40.583] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 09:22:12.017] [jointLog] [info] done
[2023-10-05 09:22:12.163] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 09:22:57.555] [jointLog] [info] Number of decoys : 194
[2023-10-05 09:22:57.555] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 09:22:59.974] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 09:23:01.041] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 09:23:45.972] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-05 09:23:46.091] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments
[2023-10-05 09:23:46.103] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-05 09:23:46.271] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-05 09:23:46.326] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-05 09:23:46.419] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-05 09:23:46.665] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-05 09:23:46.848] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-05 09:23:47.043] [jointLog] [info] Computed 67,177 rich equivalence classes for further processing
[2023-10-05 09:23:47.043] [jointLog] [info] Counted 1,721,478 total reads in the equivalence classes 
[2023-10-05 09:23:47.052] [jointLog] [info] Number of mappings discarded because of alignment score : 27,995,565
[2023-10-05 09:23:47.052] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 166,251
[2023-10-05 09:23:47.052] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 50,679
[2023-10-05 09:23:47.052] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 09:23:47.044] [fileLog] [info] 
At end of round 0
==================
Observed 2455571 total fragments (2455571 in most recent round)

[2023-10-05 09:23:48.873] [jointLog] [warning] Only 1721478 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 09:23:48.873] [jointLog] [info] Mapping rate = 70.105%

[2023-10-05 09:23:48.873] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 09:23:48.874] [jointLog] [info] Starting optimizer
[2023-10-05 09:23:55.017] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 09:23:55.420] [jointLog] [info] iteration = 0 | max rel diff. = 32.8797
[2023-10-05 09:23:59.411] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 09:24:57.411] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 09:24:57.412] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 09:25:04.585] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 09:25:11.280] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 09:25:17.992] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 09:25:24.513] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 09:25:31.242] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 09:25:37.568] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 09:25:43.263] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 09:25:48.435] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 09:25:53.273] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 09:25:58.467] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 09:26:30.009] [jointLog] [info] iteration = 100 | max rel diff. = 3.23807
[2023-10-05 09:27:05.145] [jointLog] [info] iteration = 200 | max rel diff. = 1.94562
[2023-10-05 09:27:39.687] [jointLog] [info] iteration = 300 | max rel diff. = 0.376188
[2023-10-05 09:28:14.301] [jointLog] [info] iteration = 400 | max rel diff. = 0.495983
[2023-10-05 09:28:48.897] [jointLog] [info] iteration = 500 | max rel diff. = 0.0839131
[2023-10-05 09:28:55.359] [jointLog] [info] iteration = 515 | max rel diff. = 0.00892902
[2023-10-05 09:28:57.624] [jointLog] [info] Finished optimizer
[2023-10-05 09:28:57.624] [jointLog] [info] writing output