[2023-09-25 04:21:45.694] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 04:21:45.694] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 04:21:45.694] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 04:21:45.694] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 04:21:45.694] [jointLog] [info] parsing read library format
[2023-09-25 04:21:45.694] [jointLog] [info] There is 1 library.
[2023-09-25 04:21:45.694] [jointLog] [info] Loading pufferfish index
[2023-09-25 04:21:45.694] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 04:23:03.882] [jointLog] [info] done
[2023-09-25 04:23:03.999] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 04:23:39.037] [jointLog] [info] Number of decoys : 194
[2023-09-25 04:23:39.037] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 04:23:40.150] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 04:23:41.139] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 04:24:22.303] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-09-25 04:24:22.364] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-25 04:24:22.541] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-25 04:24:22.684] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-25 04:24:22.728] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-25 04:24:22.814] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-25 04:24:22.828] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-25 04:24:22.842] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-25 04:24:23.007] [jointLog] [info] Computed 79,622 rich equivalence classes for further processing
[2023-09-25 04:24:23.007] [jointLog] [info] Counted 2,280,807 total reads in the equivalence classes 
[2023-09-25 04:24:23.014] [jointLog] [info] Number of mappings discarded because of alignment score : 54,123,674
[2023-09-25 04:24:23.014] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 276,845
[2023-09-25 04:24:23.014] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 73,724
[2023-09-25 04:24:23.014] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 04:24:23.008] [fileLog] [info] 
At end of round 0
==================
Observed 2928075 total fragments (2928075 in most recent round)

[2023-09-25 04:24:24.031] [jointLog] [warning] Only 2280807 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 04:24:24.031] [jointLog] [info] Mapping rate = 77.8944%

[2023-09-25 04:24:24.031] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 04:24:24.031] [jointLog] [info] Starting optimizer
[2023-09-25 04:24:28.028] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 04:24:28.341] [jointLog] [info] iteration = 0 | max rel diff. = 48.5548
[2023-09-25 04:24:31.500] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 04:25:23.117] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 04:25:23.118] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 04:25:28.026] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 04:25:32.599] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 04:25:37.197] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 04:25:41.952] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 04:25:46.736] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 04:25:51.254] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 04:25:56.055] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 04:26:00.594] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 04:26:05.384] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 04:26:10.164] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 04:26:39.440] [jointLog] [info] iteration = 100 | max rel diff. = 12.1679
[2023-09-25 04:27:11.738] [jointLog] [info] iteration = 200 | max rel diff. = 5.06896
[2023-09-25 04:27:43.998] [jointLog] [info] iteration = 300 | max rel diff. = 1.13
[2023-09-25 04:28:16.134] [jointLog] [info] iteration = 400 | max rel diff. = 0.0535613
[2023-09-25 04:28:48.585] [jointLog] [info] iteration = 500 | max rel diff. = 0.367563
[2023-09-25 04:29:21.232] [jointLog] [info] iteration = 600 | max rel diff. = 0.195273
[2023-09-25 04:29:53.773] [jointLog] [info] iteration = 700 | max rel diff. = 0.469154
[2023-09-25 04:30:26.248] [jointLog] [info] iteration = 800 | max rel diff. = 0.0108203
[2023-09-25 04:30:58.615] [jointLog] [info] iteration = 900 | max rel diff. = 0.0605553
[2023-09-25 04:31:04.714] [jointLog] [info] iteration = 920 | max rel diff. = 0.00782033
[2023-09-25 04:31:06.854] [jointLog] [info] Finished optimizer
[2023-09-25 04:31:06.854] [jointLog] [info] writing output