[2023-09-23 23:27:20.670] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 23:27:20.671] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 23:27:20.671] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 23:27:20.671] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 23:27:20.671] [jointLog] [info] parsing read library format
[2023-09-23 23:27:20.671] [jointLog] [info] There is 1 library.
[2023-09-23 23:27:20.671] [jointLog] [info] Loading pufferfish index
[2023-09-23 23:27:20.671] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 23:28:39.556] [jointLog] [info] done
[2023-09-23 23:28:39.703] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 23:29:19.787] [jointLog] [info] Number of decoys : 194
[2023-09-23 23:29:19.787] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 23:29:21.514] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 23:29:22.594] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 23:30:12.772] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-23 23:30:12.850] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-23 23:30:12.872] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-23 23:30:13.003] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-23 23:30:13.074] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-23 23:30:13.367] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-23 23:30:13.399] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-23 23:30:13.533] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-23 23:30:13.720] [jointLog] [info] Computed 76,561 rich equivalence classes for further processing
[2023-09-23 23:30:13.720] [jointLog] [info] Counted 2,505,356 total reads in the equivalence classes 
[2023-09-23 23:30:13.728] [jointLog] [info] Number of mappings discarded because of alignment score : 65,858,417
[2023-09-23 23:30:13.728] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 314,541
[2023-09-23 23:30:13.728] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 80,046
[2023-09-23 23:30:13.728] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 23:30:13.720] [fileLog] [info] 
At end of round 0
==================
Observed 3186979 total fragments (3186979 in most recent round)

[2023-09-23 23:30:15.376] [jointLog] [warning] Only 2505356 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 23:30:15.377] [jointLog] [info] Mapping rate = 78.6123%

[2023-09-23 23:30:15.377] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 23:30:15.377] [jointLog] [info] Starting optimizer
[2023-09-23 23:30:20.172] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 23:30:20.508] [jointLog] [info] iteration = 0 | max rel diff. = 63.4345
[2023-09-23 23:30:23.896] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 23:31:13.055] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 23:31:13.055] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 23:31:17.345] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 23:31:22.398] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 23:31:27.118] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 23:31:32.356] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 23:31:37.003] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 23:31:41.810] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 23:31:46.530] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 23:31:50.849] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 23:31:55.778] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 23:32:00.326] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 23:32:31.649] [jointLog] [info] iteration = 100 | max rel diff. = 1.74872
[2023-09-23 23:33:06.686] [jointLog] [info] iteration = 200 | max rel diff. = 0.350055
[2023-09-23 23:33:41.508] [jointLog] [info] iteration = 300 | max rel diff. = 1.47113
[2023-09-23 23:34:16.349] [jointLog] [info] iteration = 400 | max rel diff. = 0.14317
[2023-09-23 23:34:51.351] [jointLog] [info] iteration = 500 | max rel diff. = 0.039414
[2023-09-23 23:35:26.318] [jointLog] [info] iteration = 600 | max rel diff. = 0.0682596
[2023-09-23 23:36:01.008] [jointLog] [info] iteration = 700 | max rel diff. = 0.0911088
[2023-09-23 23:36:05.188] [jointLog] [info] iteration = 713 | max rel diff. = 0.00894664
[2023-09-23 23:36:07.416] [jointLog] [info] Finished optimizer
[2023-09-23 23:36:07.416] [jointLog] [info] writing output