[2023-10-03 17:30:11.673] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 17:30:11.673] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 17:30:11.673] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 17:30:11.673] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 17:30:11.673] [jointLog] [info] parsing read library format
[2023-10-03 17:30:11.673] [jointLog] [info] There is 1 library.
[2023-10-03 17:30:11.673] [jointLog] [info] Loading pufferfish index
[2023-10-03 17:30:11.673] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 17:31:37.727] [jointLog] [info] done
[2023-10-03 17:31:37.889] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 17:32:24.594] [jointLog] [info] Number of decoys : 194
[2023-10-03 17:32:24.594] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 17:32:26.714] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 17:32:27.554] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 17:33:13.637] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-03 17:33:13.667] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 17:33:13.689] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-03 17:33:13.791] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-03 17:33:13.884] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-03 17:33:13.937] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-03 17:33:14.001] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-03 17:33:14.080] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-10-03 17:33:14.244] [jointLog] [info] Computed 78,377 rich equivalence classes for further processing
[2023-10-03 17:33:14.244] [jointLog] [info] Counted 1,844,548 total reads in the equivalence classes 
[2023-10-03 17:33:14.252] [jointLog] [info] Number of mappings discarded because of alignment score : 53,153,666
[2023-10-03 17:33:14.252] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 257,515
[2023-10-03 17:33:14.252] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 65,215
[2023-10-03 17:33:14.252] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 17:33:14.245] [fileLog] [info] 
At end of round 0
==================
Observed 2634063 total fragments (2634063 in most recent round)

[2023-10-03 17:33:15.284] [jointLog] [warning] Only 1844548 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 17:33:15.284] [jointLog] [info] Mapping rate = 70.0267%

[2023-10-03 17:33:15.284] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 17:33:15.285] [jointLog] [info] Starting optimizer
[2023-10-03 17:33:20.443] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 17:33:20.792] [jointLog] [info] iteration = 0 | max rel diff. = 35.4627
[2023-10-03 17:33:24.262] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 17:34:26.111] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 17:34:26.111] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 17:34:32.291] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 17:34:38.926] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 17:34:45.876] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 17:34:53.359] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 17:35:00.414] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 17:35:06.637] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 17:35:12.682] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 17:35:18.601] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 17:35:24.184] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 17:35:29.718] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 17:35:29.723] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 17:36:01.987] [jointLog] [info] iteration = 100 | max rel diff. = 11.9318
[2023-10-03 17:36:37.460] [jointLog] [info] iteration = 200 | max rel diff. = 0.518691
[2023-10-03 17:37:16.365] [jointLog] [info] iteration = 300 | max rel diff. = 0.160692
[2023-10-03 17:37:53.279] [jointLog] [info] iteration = 400 | max rel diff. = 0.180076
[2023-10-03 17:38:28.982] [jointLog] [info] iteration = 500 | max rel diff. = 0.0263287
[2023-10-03 17:39:04.580] [jointLog] [info] iteration = 600 | max rel diff. = 0.344559
[2023-10-03 17:39:40.115] [jointLog] [info] iteration = 700 | max rel diff. = 0.55344
[2023-10-03 17:39:41.190] [jointLog] [info] iteration = 704 | max rel diff. = 0.00970759
[2023-10-03 17:39:43.346] [jointLog] [info] Finished optimizer
[2023-10-03 17:39:43.346] [jointLog] [info] writing output