[2023-09-28 01:20:18.247] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 01:20:18.247] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 01:20:18.247] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 01:20:18.247] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 01:20:18.247] [jointLog] [info] parsing read library format
[2023-09-28 01:20:18.247] [jointLog] [info] There is 1 library.
[2023-09-28 01:20:18.247] [jointLog] [info] Loading pufferfish index
[2023-09-28 01:20:18.247] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 01:21:30.237] [jointLog] [info] done
[2023-09-28 01:21:30.357] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 01:22:05.852] [jointLog] [info] Number of decoys : 194
[2023-09-28 01:22:05.852] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 01:22:07.251] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 01:22:08.872] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 01:22:53.722] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-28 01:22:53.777] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-28 01:22:53.823] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-28 01:22:53.878] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-28 01:22:53.990] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-28 01:22:54.041] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-28 01:22:54.078] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-28 01:22:54.249] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-09-28 01:22:54.440] [jointLog] [info] Computed 89,174 rich equivalence classes for further processing
[2023-09-28 01:22:54.440] [jointLog] [info] Counted 2,086,978 total reads in the equivalence classes 
[2023-09-28 01:22:54.441] [fileLog] [info] 
At end of round 0
==================
Observed 2867039 total fragments (2867039 in most recent round)

[2023-09-28 01:22:54.449] [jointLog] [info] Number of mappings discarded because of alignment score : 53,576,674
[2023-09-28 01:22:54.449] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 229,445
[2023-09-28 01:22:54.449] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 39,130
[2023-09-28 01:22:54.449] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 01:22:55.534] [jointLog] [warning] Only 2086978 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 01:22:55.534] [jointLog] [info] Mapping rate = 72.7921%

[2023-09-28 01:22:55.534] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 01:22:55.535] [jointLog] [info] Starting optimizer
[2023-09-28 01:22:59.264] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 01:22:59.586] [jointLog] [info] iteration = 0 | max rel diff. = 40.4697
[2023-09-28 01:23:02.849] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 01:23:55.606] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 01:23:55.606] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 01:24:00.052] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 01:24:04.772] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 01:24:10.052] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 01:24:14.829] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 01:24:19.639] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 01:24:24.700] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 01:24:29.618] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 01:24:34.542] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 01:24:39.518] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 01:24:43.997] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 01:25:12.549] [jointLog] [info] iteration = 100 | max rel diff. = 5.0009
[2023-09-28 01:25:43.948] [jointLog] [info] iteration = 200 | max rel diff. = 1.5196
[2023-09-28 01:26:15.380] [jointLog] [info] iteration = 300 | max rel diff. = 1.13278
[2023-09-28 01:26:46.770] [jointLog] [info] iteration = 400 | max rel diff. = 1.26961
[2023-09-28 01:27:18.118] [jointLog] [info] iteration = 500 | max rel diff. = 0.269509
[2023-09-28 01:27:49.308] [jointLog] [info] iteration = 600 | max rel diff. = 0.380562
[2023-09-28 01:27:55.831] [jointLog] [info] iteration = 622 | max rel diff. = 0.00581975
[2023-09-28 01:27:57.924] [jointLog] [info] Finished optimizer
[2023-09-28 01:27:57.924] [jointLog] [info] writing output