[2023-09-23 21:52:53.808] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 21:52:53.808] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 21:52:53.808] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 21:52:53.808] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 21:52:53.808] [jointLog] [info] parsing read library format
[2023-09-23 21:52:53.808] [jointLog] [info] There is 1 library.
[2023-09-23 21:52:53.808] [jointLog] [info] Loading pufferfish index
[2023-09-23 21:52:53.808] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 21:54:06.638] [jointLog] [info] done
[2023-09-23 21:54:06.762] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 21:54:42.249] [jointLog] [info] Number of decoys : 194
[2023-09-23 21:54:42.249] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 21:54:43.258] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 21:54:44.378] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 21:55:54.302] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-23 21:55:54.330] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-09-23 21:55:54.627] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-23 21:55:54.696] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-23 21:55:54.739] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-23 21:55:54.895] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-23 21:55:54.923] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-23 21:55:55.025] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-23 21:55:55.174] [jointLog] [info] Computed 86,147 rich equivalence classes for further processing
[2023-09-23 21:55:55.174] [jointLog] [info] Counted 3,304,516 total reads in the equivalence classes 
[2023-09-23 21:55:55.181] [jointLog] [info] Number of mappings discarded because of alignment score : 102,761,574
[2023-09-23 21:55:55.181] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 456,471
[2023-09-23 21:55:55.181] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 120,462
[2023-09-23 21:55:55.181] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 21:55:55.175] [fileLog] [info] 
At end of round 0
==================
Observed 4223538 total fragments (4223538 in most recent round)

[2023-09-23 21:55:56.178] [jointLog] [warning] Only 3304516 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 21:55:56.178] [jointLog] [info] Mapping rate = 78.2405%

[2023-09-23 21:55:56.178] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 21:55:56.178] [jointLog] [info] Starting optimizer
[2023-09-23 21:55:59.766] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 21:56:00.084] [jointLog] [info] iteration = 0 | max rel diff. = 59.3902
[2023-09-23 21:56:03.279] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 21:56:54.358] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 21:56:54.358] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 21:56:58.823] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 21:57:03.308] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 21:57:07.897] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 21:57:12.713] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 21:57:17.346] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 21:57:21.937] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 21:57:26.327] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 21:57:31.124] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 21:57:35.679] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 21:57:40.518] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 21:58:10.192] [jointLog] [info] iteration = 100 | max rel diff. = 13.506
[2023-09-23 21:58:42.070] [jointLog] [info] iteration = 200 | max rel diff. = 2.18512
[2023-09-23 21:59:13.826] [jointLog] [info] iteration = 300 | max rel diff. = 0.317764
[2023-09-23 21:59:45.966] [jointLog] [info] iteration = 400 | max rel diff. = 12.989
[2023-09-23 22:00:18.151] [jointLog] [info] iteration = 500 | max rel diff. = 0.0827327
[2023-09-23 22:00:49.983] [jointLog] [info] iteration = 600 | max rel diff. = 0.552838
[2023-09-23 22:01:23.179] [jointLog] [info] iteration = 700 | max rel diff. = 0.287397
[2023-09-23 22:01:46.087] [jointLog] [info] iteration = 774 | max rel diff. = 0.0082703
[2023-09-23 22:01:48.116] [jointLog] [info] Finished optimizer
[2023-09-23 22:01:48.116] [jointLog] [info] writing output