[2023-09-25 13:43:37.596] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 13:43:37.596] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 13:43:37.596] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 13:43:37.596] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 13:43:37.596] [jointLog] [info] parsing read library format
[2023-09-25 13:43:37.596] [jointLog] [info] There is 1 library.
[2023-09-25 13:43:37.597] [jointLog] [info] Loading pufferfish index
[2023-09-25 13:43:37.597] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 13:44:54.217] [jointLog] [info] done
[2023-09-25 13:44:54.374] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 13:45:34.802] [jointLog] [info] Number of decoys : 194
[2023-09-25 13:45:34.802] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 13:45:36.898] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 13:45:38.466] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 13:46:25.322] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-25 13:46:25.486] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-25 13:46:25.486] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-25 13:46:25.605] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-09-25 13:46:25.658] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-25 13:46:25.685] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-09-25 13:46:25.728] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-25 13:46:25.812] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-25 13:46:25.978] [jointLog] [info] Computed 75,101 rich equivalence classes for further processing
[2023-09-25 13:46:25.978] [jointLog] [info] Counted 1,986,257 total reads in the equivalence classes 
[2023-09-25 13:46:25.986] [jointLog] [info] Number of mappings discarded because of alignment score : 61,626,729
[2023-09-25 13:46:25.986] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 264,534
[2023-09-25 13:46:25.986] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 73,177
[2023-09-25 13:46:25.986] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 13:46:25.979] [fileLog] [info] 
At end of round 0
==================
Observed 2622813 total fragments (2622813 in most recent round)

[2023-09-25 13:46:27.065] [jointLog] [warning] Only 1986257 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 13:46:27.065] [jointLog] [info] Mapping rate = 75.73%

[2023-09-25 13:46:27.065] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 13:46:27.065] [jointLog] [info] Starting optimizer
[2023-09-25 13:46:32.628] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 13:46:32.990] [jointLog] [info] iteration = 0 | max rel diff. = 43.5378
[2023-09-25 13:46:36.331] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 13:47:26.167] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 13:47:26.167] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 13:47:30.373] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 13:47:34.987] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 13:47:39.516] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 13:47:44.303] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 13:47:49.016] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 13:47:53.715] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 13:47:58.373] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 13:48:03.228] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 13:48:07.856] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 13:48:12.342] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 13:48:42.523] [jointLog] [info] iteration = 100 | max rel diff. = 1.35343
[2023-09-25 13:49:15.403] [jointLog] [info] iteration = 200 | max rel diff. = 0.927181
[2023-09-25 13:49:48.387] [jointLog] [info] iteration = 300 | max rel diff. = 20.3189
[2023-09-25 13:50:21.334] [jointLog] [info] iteration = 400 | max rel diff. = 0.133968
[2023-09-25 13:50:54.293] [jointLog] [info] iteration = 500 | max rel diff. = 0.530877
[2023-09-25 13:51:26.535] [jointLog] [info] iteration = 600 | max rel diff. = 0.144058
[2023-09-25 13:51:59.128] [jointLog] [info] iteration = 700 | max rel diff. = 0.0254522
[2023-09-25 13:52:13.260] [jointLog] [info] iteration = 744 | max rel diff. = 0.00801436
[2023-09-25 13:52:15.727] [jointLog] [info] Finished optimizer
[2023-09-25 13:52:15.727] [jointLog] [info] writing output