[2023-09-28 09:23:33.344] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 09:23:33.344] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 09:23:33.344] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 09:23:33.344] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 09:23:33.344] [jointLog] [info] parsing read library format
[2023-09-28 09:23:33.344] [jointLog] [info] There is 1 library.
[2023-09-28 09:23:33.344] [jointLog] [info] Loading pufferfish index
[2023-09-28 09:23:33.344] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 09:24:53.155] [jointLog] [info] done
[2023-09-28 09:24:53.285] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 09:25:30.187] [jointLog] [info] Number of decoys : 194
[2023-09-28 09:25:30.187] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 09:25:31.715] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 09:25:32.633] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 09:25:57.796] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-28 09:25:57.843] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-28 09:25:57.888] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-28 09:25:57.942] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-28 09:25:57.999] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-28 09:25:58.064] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-28 09:25:58.160] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-28 09:25:58.209] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-28 09:25:58.436] [fileLog] [info] 
At end of round 0
==================
Observed 1739310 total fragments (1739310 in most recent round)

[2023-09-28 09:25:58.435] [jointLog] [info] Computed 75,872 rich equivalence classes for further processing
[2023-09-28 09:25:58.435] [jointLog] [info] Counted 1,324,206 total reads in the equivalence classes 
[2023-09-28 09:25:58.443] [jointLog] [warning] 0.000114988% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 10.


[2023-09-28 09:25:58.443] [jointLog] [info] Number of mappings discarded because of alignment score : 21,788,448
[2023-09-28 09:25:58.443] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 139,336
[2023-09-28 09:25:58.443] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 43,659
[2023-09-28 09:25:58.443] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 09:25:59.344] [jointLog] [warning] Only 1324206 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-28 09:25:59.344] [jointLog] [info] Mapping rate = 76.134%

[2023-09-28 09:25:59.344] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 09:25:59.345] [jointLog] [info] Starting optimizer
[2023-09-28 09:26:03.567] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 09:26:03.904] [jointLog] [info] iteration = 0 | max rel diff. = 25.3625
[2023-09-28 09:26:07.289] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 09:27:07.941] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 09:27:07.942] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 09:27:15.595] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 09:27:20.088] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 09:27:25.080] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 09:27:30.178] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 09:27:34.939] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 09:27:40.170] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 09:27:44.956] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 09:27:49.824] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 09:27:54.979] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 09:28:00.125] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 09:28:00.161] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 09:28:30.337] [jointLog] [info] iteration = 100 | max rel diff. = 1.97207
[2023-09-28 09:29:04.272] [jointLog] [info] iteration = 200 | max rel diff. = 0.595492
[2023-09-28 09:29:38.304] [jointLog] [info] iteration = 300 | max rel diff. = 0.175129
[2023-09-28 09:30:12.238] [jointLog] [info] iteration = 400 | max rel diff. = 0.462015
[2023-09-28 09:30:46.671] [jointLog] [info] iteration = 500 | max rel diff. = 1.53233
[2023-09-28 09:31:21.032] [jointLog] [info] iteration = 600 | max rel diff. = 0.0150396
[2023-09-28 09:31:45.883] [jointLog] [info] iteration = 673 | max rel diff. = 0.0085478
[2023-09-28 09:31:47.701] [jointLog] [info] Finished optimizer
[2023-09-28 09:31:47.701] [jointLog] [info] writing output