[2023-10-03 06:34:47.538] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 06:34:47.538] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 06:34:47.538] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 06:34:47.538] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 06:34:47.538] [jointLog] [info] parsing read library format
[2023-10-03 06:34:47.538] [jointLog] [info] There is 1 library.
[2023-10-03 06:34:47.539] [jointLog] [info] Loading pufferfish index
[2023-10-03 06:34:47.539] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 06:36:03.682] [jointLog] [info] done
[2023-10-03 06:36:03.805] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 06:36:42.764] [jointLog] [info] Number of decoys : 194
[2023-10-03 06:36:42.764] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 06:36:44.649] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 06:36:45.722] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 06:37:46.790] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 06:37:46.863] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-03 06:37:46.909] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-03 06:37:46.928] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-10-03 06:37:47.057] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 06:37:47.075] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 06:37:47.231] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 06:37:47.262] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-03 06:37:47.506] [fileLog] [info] 
At end of round 0
==================
Observed 3861255 total fragments (3861255 in most recent round)

[2023-10-03 06:37:47.505] [jointLog] [info] Computed 108,719 rich equivalence classes for further processing
[2023-10-03 06:37:47.505] [jointLog] [info] Counted 2,926,220 total reads in the equivalence classes 
[2023-10-03 06:37:47.513] [jointLog] [info] Number of mappings discarded because of alignment score : 60,524,740
[2023-10-03 06:37:47.513] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 356,762
[2023-10-03 06:37:47.513] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 83,384
[2023-10-03 06:37:47.513] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 06:37:48.863] [jointLog] [warning] Only 2926220 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 06:37:48.863] [jointLog] [info] Mapping rate = 75.7842%

[2023-10-03 06:37:48.863] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 06:37:48.864] [jointLog] [info] Starting optimizer
[2023-10-03 06:37:54.117] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 06:37:54.452] [jointLog] [info] iteration = 0 | max rel diff. = 55.1593
[2023-10-03 06:37:57.823] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 06:39:01.156] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 06:39:01.157] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 06:39:06.943] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 06:39:12.587] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 06:39:18.482] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 06:39:24.560] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 06:39:30.527] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 06:39:36.385] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 06:39:42.199] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 06:39:47.819] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 06:39:53.911] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 06:39:59.495] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 06:39:59.519] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 06:40:29.450] [jointLog] [info] iteration = 100 | max rel diff. = 6.99476
[2023-10-03 06:41:02.471] [jointLog] [info] iteration = 200 | max rel diff. = 16.034
[2023-10-03 06:41:35.361] [jointLog] [info] iteration = 300 | max rel diff. = 5.64201
[2023-10-03 06:42:08.423] [jointLog] [info] iteration = 400 | max rel diff. = 0.957167
[2023-10-03 06:42:41.659] [jointLog] [info] iteration = 500 | max rel diff. = 0.331283
[2023-10-03 06:43:15.045] [jointLog] [info] iteration = 600 | max rel diff. = 0.0166837
[2023-10-03 06:43:48.670] [jointLog] [info] iteration = 700 | max rel diff. = 0.207089
[2023-10-03 06:44:22.411] [jointLog] [info] iteration = 800 | max rel diff. = 0.0148497
[2023-10-03 06:44:55.605] [jointLog] [info] iteration = 900 | max rel diff. = 0.0294651
[2023-10-03 06:45:28.533] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0346799
[2023-10-03 06:45:38.103] [jointLog] [info] iteration = 1,030 | max rel diff. = 0.0076483
[2023-10-03 06:45:40.342] [jointLog] [info] Finished optimizer
[2023-10-03 06:45:40.342] [jointLog] [info] writing output