[2023-09-26 17:23:04.972] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 17:23:04.972] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 17:23:04.972] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 17:23:04.972] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 17:23:04.972] [jointLog] [info] parsing read library format
[2023-09-26 17:23:04.972] [jointLog] [info] There is 1 library.
[2023-09-26 17:23:04.973] [jointLog] [info] Loading pufferfish index
[2023-09-26 17:23:04.973] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 17:24:18.695] [jointLog] [info] done
[2023-09-26 17:24:18.816] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 17:24:54.893] [jointLog] [info] Number of decoys : 194
[2023-09-26 17:24:54.893] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 17:24:56.121] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 17:24:57.348] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 17:25:39.476] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-09-26 17:25:39.491] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-26 17:25:39.492] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-09-26 17:25:39.497] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-09-26 17:25:39.509] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-09-26 17:25:39.516] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-26 17:25:39.520] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-26 17:25:39.949] [fileLog] [info] 
At end of round 0
==================
Observed 3402335 total fragments (3402335 in most recent round)

[2023-09-26 17:25:39.783] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-09-26 17:25:39.948] [jointLog] [info] Computed 102,898 rich equivalence classes for further processing
[2023-09-26 17:25:39.948] [jointLog] [info] Counted 2,606,548 total reads in the equivalence classes 
[2023-09-26 17:25:39.957] [jointLog] [info] Number of mappings discarded because of alignment score : 41,501,241
[2023-09-26 17:25:39.957] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 233,584
[2023-09-26 17:25:39.957] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 60,141
[2023-09-26 17:25:39.957] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 17:25:40.708] [jointLog] [warning] Only 2606548 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 17:25:40.708] [jointLog] [info] Mapping rate = 76.6106%

[2023-09-26 17:25:40.708] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 17:25:40.708] [jointLog] [info] Starting optimizer
[2023-09-26 17:25:44.315] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 17:25:44.645] [jointLog] [info] iteration = 0 | max rel diff. = 50.0991
[2023-09-26 17:25:48.122] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 17:26:45.259] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 17:26:45.260] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 17:26:50.259] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 17:26:55.512] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 17:27:00.709] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 17:27:06.071] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 17:27:11.098] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 17:27:16.559] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 17:27:21.695] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 17:27:26.901] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 17:27:31.915] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 17:27:36.994] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 17:28:06.001] [jointLog] [info] iteration = 100 | max rel diff. = 4.27188
[2023-09-26 17:28:38.482] [jointLog] [info] iteration = 200 | max rel diff. = 0.268499
[2023-09-26 17:29:10.896] [jointLog] [info] iteration = 300 | max rel diff. = 0.246776
[2023-09-26 17:29:42.942] [jointLog] [info] iteration = 400 | max rel diff. = 0.153401
[2023-09-26 17:30:15.129] [jointLog] [info] iteration = 500 | max rel diff. = 0.0517302
[2023-09-26 17:30:47.571] [jointLog] [info] iteration = 600 | max rel diff. = 0.0389931
[2023-09-26 17:31:20.047] [jointLog] [info] iteration = 700 | max rel diff. = 0.0678772
[2023-09-26 17:31:52.487] [jointLog] [info] iteration = 800 | max rel diff. = 0.00359994
[2023-09-26 17:31:52.487] [jointLog] [info] iteration = 801 | max rel diff. = 0.00359994
[2023-09-26 17:31:54.246] [jointLog] [info] Finished optimizer
[2023-09-26 17:31:54.246] [jointLog] [info] writing output