[2023-09-21 16:16:21.267] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 16:16:21.267] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 16:16:21.267] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 16:16:21.267] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 16:16:21.267] [jointLog] [info] parsing read library format
[2023-09-21 16:16:21.267] [jointLog] [info] There is 1 library.
[2023-09-21 16:16:21.268] [jointLog] [info] Loading pufferfish index
[2023-09-21 16:16:21.268] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 16:17:42.086] [jointLog] [info] done
[2023-09-21 16:17:42.245] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 16:18:22.387] [jointLog] [info] Number of decoys : 194
[2023-09-21 16:18:22.387] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 16:18:24.919] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 16:18:25.943] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 16:19:04.236] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-21 16:19:04.323] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-09-21 16:19:04.378] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-09-21 16:19:04.380] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-21 16:19:04.405] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-21 16:19:04.964] [fileLog] [info] 
At end of round 0
==================
Observed 2336969 total fragments (2336969 in most recent round)

[2023-09-21 16:19:04.694] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-09-21 16:19:04.707] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-21 16:19:04.767] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-21 16:19:04.963] [jointLog] [info] Computed 72,288 rich equivalence classes for further processing
[2023-09-21 16:19:04.963] [jointLog] [info] Counted 1,692,061 total reads in the equivalence classes 
[2023-09-21 16:19:04.978] [jointLog] [info] Number of mappings discarded because of alignment score : 49,771,146
[2023-09-21 16:19:04.978] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 276,743
[2023-09-21 16:19:04.978] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 52,704
[2023-09-21 16:19:04.978] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 16:19:06.250] [jointLog] [warning] Only 1692061 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 16:19:06.250] [jointLog] [info] Mapping rate = 72.4041%

[2023-09-21 16:19:06.250] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 16:19:06.250] [jointLog] [info] Starting optimizer
[2023-09-21 16:19:11.281] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 16:19:11.618] [jointLog] [info] iteration = 0 | max rel diff. = 31.0653
[2023-09-21 16:19:14.974] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 16:20:02.915] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 16:20:02.916] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 16:20:07.140] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 16:20:11.496] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 16:20:15.572] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 16:20:19.990] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 16:20:24.467] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 16:20:28.914] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 16:20:33.044] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 16:20:36.903] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 16:20:41.127] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 16:20:45.558] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 16:21:15.457] [jointLog] [info] iteration = 100 | max rel diff. = 7.79132
[2023-09-21 16:21:48.410] [jointLog] [info] iteration = 200 | max rel diff. = 7.74832
[2023-09-21 16:22:21.532] [jointLog] [info] iteration = 300 | max rel diff. = 1.02458
[2023-09-21 16:22:54.851] [jointLog] [info] iteration = 400 | max rel diff. = 0.829896
[2023-09-21 16:23:28.090] [jointLog] [info] iteration = 500 | max rel diff. = 0.253212
[2023-09-21 16:24:00.868] [jointLog] [info] iteration = 600 | max rel diff. = 0.0379522
[2023-09-21 16:24:33.039] [jointLog] [info] iteration = 700 | max rel diff. = 0.0332958
[2023-09-21 16:24:44.009] [jointLog] [info] iteration = 736 | max rel diff. = 0.00367919
[2023-09-21 16:24:46.753] [jointLog] [info] Finished optimizer
[2023-09-21 16:24:46.753] [jointLog] [info] writing output