[2023-10-02 19:13:31.679] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 19:13:31.679] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 19:13:31.680] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 19:13:31.680] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 19:13:31.680] [jointLog] [info] parsing read library format
[2023-10-02 19:13:31.680] [jointLog] [info] There is 1 library.
[2023-10-02 19:13:31.680] [jointLog] [info] Loading pufferfish index
[2023-10-02 19:13:31.680] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 19:14:46.445] [jointLog] [info] done
[2023-10-02 19:14:46.615] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 19:15:27.872] [jointLog] [info] Number of decoys : 194
[2023-10-02 19:15:27.872] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 19:15:29.580] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 19:15:30.825] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 19:16:21.717] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-02 19:16:21.752] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-10-02 19:16:21.934] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-02 19:16:21.985] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-02 19:16:22.068] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-10-02 19:16:22.082] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-02 19:16:22.124] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-02 19:16:22.149] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-10-02 19:16:22.392] [fileLog] [info] 
At end of round 0
==================
Observed 2946455 total fragments (2946455 in most recent round)

[2023-10-02 19:16:22.390] [jointLog] [info] Computed 87,536 rich equivalence classes for further processing
[2023-10-02 19:16:22.390] [jointLog] [info] Counted 2,277,956 total reads in the equivalence classes 
[2023-10-02 19:16:22.406] [jointLog] [info] Number of mappings discarded because of alignment score : 56,549,412
[2023-10-02 19:16:22.406] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 287,790
[2023-10-02 19:16:22.406] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 66,075
[2023-10-02 19:16:22.406] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 19:16:23.828] [jointLog] [warning] Only 2277956 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-02 19:16:23.828] [jointLog] [info] Mapping rate = 77.3118%

[2023-10-02 19:16:23.828] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 19:16:23.828] [jointLog] [info] Starting optimizer
[2023-10-02 19:16:29.819] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 19:16:30.206] [jointLog] [info] iteration = 0 | max rel diff. = 41.8619
[2023-10-02 19:16:33.864] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 19:17:29.440] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 19:17:29.441] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 19:17:35.350] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 19:17:41.823] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 19:17:48.048] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 19:17:54.192] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 19:17:59.952] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 19:18:05.012] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 19:18:10.038] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 19:18:14.963] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 19:18:20.488] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 19:18:25.438] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 19:18:56.319] [jointLog] [info] iteration = 100 | max rel diff. = 10.3672
[2023-10-02 19:19:30.603] [jointLog] [info] iteration = 200 | max rel diff. = 0.167229
[2023-10-02 19:20:04.685] [jointLog] [info] iteration = 300 | max rel diff. = 0.455162
[2023-10-02 19:20:38.002] [jointLog] [info] iteration = 400 | max rel diff. = 0.181754
[2023-10-02 19:21:11.966] [jointLog] [info] iteration = 500 | max rel diff. = 0.118267
[2023-10-02 19:21:45.860] [jointLog] [info] iteration = 600 | max rel diff. = 0.0269892
[2023-10-02 19:22:20.720] [jointLog] [info] iteration = 700 | max rel diff. = 0.0388765
[2023-10-02 19:22:43.244] [jointLog] [info] iteration = 766 | max rel diff. = 0.00562576
[2023-10-02 19:22:45.203] [jointLog] [info] Finished optimizer
[2023-10-02 19:22:45.203] [jointLog] [info] writing output