[2023-10-04 17:13:45.022] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 17:13:45.022] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 17:13:45.023] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 17:13:45.023] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 17:13:45.023] [jointLog] [info] parsing read library format
[2023-10-04 17:13:45.023] [jointLog] [info] There is 1 library.
[2023-10-04 17:13:45.023] [jointLog] [info] Loading pufferfish index
[2023-10-04 17:13:45.023] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 17:15:00.203] [jointLog] [info] done
[2023-10-04 17:15:00.363] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 17:15:46.630] [jointLog] [info] Number of decoys : 194
[2023-10-04 17:15:46.630] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 17:15:49.152] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 17:15:50.107] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 17:16:43.896] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2023-10-04 17:16:43.965] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 17:16:43.997] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-04 17:16:43.998] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-04 17:16:44.041] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-04 17:16:44.104] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 17:16:44.164] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-04 17:16:44.241] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 17:16:44.427] [jointLog] [info] Computed 75,032 rich equivalence classes for further processing
[2023-10-04 17:16:44.427] [jointLog] [info] Counted 3,193,163 total reads in the equivalence classes 
[2023-10-04 17:16:44.434] [jointLog] [info] Number of mappings discarded because of alignment score : 50,355,769
[2023-10-04 17:16:44.434] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 331,099
[2023-10-04 17:16:44.434] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 102,929
[2023-10-04 17:16:44.434] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 17:16:44.428] [fileLog] [info] 
At end of round 0
==================
Observed 4166016 total fragments (4166016 in most recent round)

[2023-10-04 17:16:45.491] [jointLog] [warning] Only 3193163 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 17:16:45.491] [jointLog] [info] Mapping rate = 76.6479%

[2023-10-04 17:16:45.491] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 17:16:45.492] [jointLog] [info] Starting optimizer
[2023-10-04 17:16:50.106] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 17:16:50.467] [jointLog] [info] iteration = 0 | max rel diff. = 60.2808
[2023-10-04 17:16:54.030] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 17:17:45.493] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 17:17:45.494] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 17:17:49.909] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 17:17:54.113] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 17:17:58.543] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 17:18:03.336] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 17:18:08.022] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 17:18:13.041] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 17:18:17.878] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 17:18:22.716] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 17:18:27.421] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 17:18:31.885] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 17:19:02.426] [jointLog] [info] iteration = 100 | max rel diff. = 13.7694
[2023-10-04 17:19:36.991] [jointLog] [info] iteration = 200 | max rel diff. = 1.93626
[2023-10-04 17:20:11.141] [jointLog] [info] iteration = 300 | max rel diff. = 0.116253
[2023-10-04 17:20:45.895] [jointLog] [info] iteration = 400 | max rel diff. = 0.224908
[2023-10-04 17:21:20.874] [jointLog] [info] iteration = 500 | max rel diff. = 0.850402
[2023-10-04 17:21:55.998] [jointLog] [info] iteration = 600 | max rel diff. = 0.0223532
[2023-10-04 17:22:31.211] [jointLog] [info] iteration = 700 | max rel diff. = 2.07447
[2023-10-04 17:23:05.992] [jointLog] [info] iteration = 800 | max rel diff. = 0.443128
[2023-10-04 17:23:41.679] [jointLog] [info] iteration = 900 | max rel diff. = 0.0103733
[2023-10-04 17:24:17.130] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0790724
[2023-10-04 17:24:25.624] [jointLog] [info] iteration = 1,025 | max rel diff. = 0.00268786
[2023-10-04 17:24:27.470] [jointLog] [info] Finished optimizer
[2023-10-04 17:24:27.470] [jointLog] [info] writing output