[2023-09-25 07:18:10.679] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 07:18:10.679] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 07:18:10.679] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 07:18:10.679] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 07:18:10.679] [jointLog] [info] parsing read library format
[2023-09-25 07:18:10.679] [jointLog] [info] There is 1 library.
[2023-09-25 07:18:10.680] [jointLog] [info] Loading pufferfish index
[2023-09-25 07:18:10.680] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 07:19:32.512] [jointLog] [info] done
[2023-09-25 07:19:32.631] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 07:20:08.869] [jointLog] [info] Number of decoys : 194
[2023-09-25 07:20:08.869] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 07:20:10.556] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 07:20:11.386] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 07:20:42.473] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-25 07:20:42.515] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-25 07:20:42.533] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-25 07:20:42.546] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-25 07:20:42.797] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-25 07:20:42.808] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-25 07:20:42.954] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-25 07:20:43.023] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-09-25 07:20:43.176] [jointLog] [info] Computed 65,832 rich equivalence classes for further processing
[2023-09-25 07:20:43.176] [jointLog] [info] Counted 1,553,491 total reads in the equivalence classes 
[2023-09-25 07:20:43.184] [jointLog] [info] Number of mappings discarded because of alignment score : 40,991,995
[2023-09-25 07:20:43.184] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 205,457
[2023-09-25 07:20:43.184] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 61,858
[2023-09-25 07:20:43.184] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 07:20:43.177] [fileLog] [info] 
At end of round 0
==================
Observed 2145979 total fragments (2145979 in most recent round)

[2023-09-25 07:20:44.254] [jointLog] [warning] Only 1553491 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 07:20:44.254] [jointLog] [info] Mapping rate = 72.3908%

[2023-09-25 07:20:44.254] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 07:20:44.254] [jointLog] [info] Starting optimizer
[2023-09-25 07:20:48.051] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 07:20:48.370] [jointLog] [info] iteration = 0 | max rel diff. = 29.8456
[2023-09-25 07:20:51.656] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 07:21:36.802] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 07:21:36.802] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 07:21:40.570] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 07:21:44.963] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 07:21:49.294] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 07:21:53.574] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 07:21:58.011] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 07:22:02.307] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 07:22:06.840] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 07:22:11.024] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 07:22:15.109] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 07:22:19.216] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 07:22:48.420] [jointLog] [info] iteration = 100 | max rel diff. = 8.08256
[2023-09-25 07:23:20.265] [jointLog] [info] iteration = 200 | max rel diff. = 0.26684
[2023-09-25 07:23:51.635] [jointLog] [info] iteration = 300 | max rel diff. = 4.3343
[2023-09-25 07:24:22.904] [jointLog] [info] iteration = 400 | max rel diff. = 0.120827
[2023-09-25 07:24:47.201] [jointLog] [info] iteration = 478 | max rel diff. = 0.00808311
[2023-09-25 07:24:49.421] [jointLog] [info] Finished optimizer
[2023-09-25 07:24:49.421] [jointLog] [info] writing output