[2023-09-21 23:31:11.069] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 23:31:11.069] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 23:31:11.069] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 23:31:11.069] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 23:31:11.069] [jointLog] [info] parsing read library format
[2023-09-21 23:31:11.069] [jointLog] [info] There is 1 library.
[2023-09-21 23:31:11.069] [jointLog] [info] Loading pufferfish index
[2023-09-21 23:31:11.069] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 23:32:23.297] [jointLog] [info] done
[2023-09-21 23:32:23.421] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 23:33:01.105] [jointLog] [info] Number of decoys : 194
[2023-09-21 23:33:01.105] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 23:33:02.926] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 23:33:04.089] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 23:33:12.440] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-21 23:33:12.456] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-21 23:33:12.487] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-21 23:33:12.608] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-21 23:33:12.693] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-21 23:33:12.754] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-21 23:33:12.773] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-21 23:33:12.825] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-21 23:33:12.924] [jointLog] [info] Computed 35,398 rich equivalence classes for further processing
[2023-09-21 23:33:12.924] [jointLog] [info] Counted 490,336 total reads in the equivalence classes 
[2023-09-21 23:33:12.934] [jointLog] [info] Number of mappings discarded because of alignment score : 10,180,812
[2023-09-21 23:33:12.934] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 52,422
[2023-09-21 23:33:12.934] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 14,643
[2023-09-21 23:33:12.934] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 23:33:12.925] [fileLog] [info] 
At end of round 0
==================
Observed 662495 total fragments (662495 in most recent round)

[2023-09-21 23:33:13.730] [jointLog] [warning] Only 490336 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 23:33:13.730] [jointLog] [info] Mapping rate = 74.0135%

[2023-09-21 23:33:13.730] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 23:33:13.818] [jointLog] [info] Starting optimizer
[2023-09-21 23:33:17.781] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 23:33:18.109] [jointLog] [info] iteration = 0 | max rel diff. = 9.55258
[2023-09-21 23:33:21.404] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 23:33:51.235] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 23:33:51.236] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 23:33:53.826] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 23:33:56.430] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 23:33:59.139] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 23:34:02.033] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 23:34:04.551] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 23:34:07.513] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 23:34:10.374] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 23:34:12.919] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 23:34:15.776] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 23:34:18.568] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 23:34:48.867] [jointLog] [info] iteration = 100 | max rel diff. = 5.82889
[2023-09-21 23:35:22.123] [jointLog] [info] iteration = 200 | max rel diff. = 0.149225
[2023-09-21 23:35:55.661] [jointLog] [info] iteration = 300 | max rel diff. = 0.170182
[2023-09-21 23:36:19.942] [jointLog] [info] iteration = 373 | max rel diff. = 0.00932358
[2023-09-21 23:36:22.077] [jointLog] [info] Finished optimizer
[2023-09-21 23:36:22.077] [jointLog] [info] writing output