[2023-10-03 09:26:39.417] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 09:26:39.417] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 09:26:39.417] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 09:26:39.417] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 09:26:39.417] [jointLog] [info] parsing read library format
[2023-10-03 09:26:39.417] [jointLog] [info] There is 1 library.
[2023-10-03 09:26:39.417] [jointLog] [info] Loading pufferfish index
[2023-10-03 09:26:39.417] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 09:28:02.221] [jointLog] [info] done
[2023-10-03 09:28:02.378] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 09:28:43.186] [jointLog] [info] Number of decoys : 194
[2023-10-03 09:28:43.186] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 09:28:45.055] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 09:28:46.341] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 09:29:31.285] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-03 09:29:31.349] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-03 09:29:31.389] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-10-03 09:29:31.469] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-10-03 09:29:31.554] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-10-03 09:29:31.639] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-10-03 09:29:31.775] [jointLog] [info] Thread saw mini-batch with a maximum of 2.66% zero probability fragments
[2023-10-03 09:29:31.834] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-03 09:29:32.047] [fileLog] [info] 
At end of round 0
==================
Observed 3116467 total fragments (3116467 in most recent round)

[2023-10-03 09:29:32.046] [jointLog] [info] Computed 88,295 rich equivalence classes for further processing
[2023-10-03 09:29:32.046] [jointLog] [info] Counted 2,370,302 total reads in the equivalence classes 
[2023-10-03 09:29:32.055] [jointLog] [info] Number of mappings discarded because of alignment score : 46,122,159
[2023-10-03 09:29:32.055] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 295,318
[2023-10-03 09:29:32.055] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 64,249
[2023-10-03 09:29:32.055] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 09:29:33.833] [jointLog] [warning] Only 2370302 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 09:29:33.833] [jointLog] [info] Mapping rate = 76.0573%

[2023-10-03 09:29:33.833] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 09:29:33.834] [jointLog] [info] Starting optimizer
[2023-10-03 09:29:39.024] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 09:29:39.360] [jointLog] [info] iteration = 0 | max rel diff. = 46.232
[2023-10-03 09:29:42.787] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 09:30:37.124] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 09:30:37.125] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 09:30:41.600] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 09:30:46.617] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 09:30:51.991] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 09:30:56.961] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 09:31:02.039] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 09:31:07.092] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 09:31:12.224] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 09:31:17.295] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 09:31:22.162] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 09:31:26.935] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 09:31:57.783] [jointLog] [info] iteration = 100 | max rel diff. = 1.05542
[2023-10-03 09:32:31.001] [jointLog] [info] iteration = 200 | max rel diff. = 3.4539
[2023-10-03 09:33:04.209] [jointLog] [info] iteration = 300 | max rel diff. = 0.30997
[2023-10-03 09:33:37.143] [jointLog] [info] iteration = 400 | max rel diff. = 0.0471733
[2023-10-03 09:34:10.479] [jointLog] [info] iteration = 500 | max rel diff. = 0.0269112
[2023-10-03 09:34:43.772] [jointLog] [info] iteration = 600 | max rel diff. = 0.0518613
[2023-10-03 09:35:16.778] [jointLog] [info] iteration = 700 | max rel diff. = 0.108476
[2023-10-03 09:35:49.885] [jointLog] [info] iteration = 800 | max rel diff. = 0.0254633
[2023-10-03 09:36:01.943] [jointLog] [info] iteration = 837 | max rel diff. = 0.00581806
[2023-10-03 09:36:04.011] [jointLog] [info] Finished optimizer
[2023-10-03 09:36:04.011] [jointLog] [info] writing output