[2023-10-03 16:21:28.130] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 16:21:28.130] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 16:21:28.130] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 16:21:28.130] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 16:21:28.130] [jointLog] [info] parsing read library format
[2023-10-03 16:21:28.130] [jointLog] [info] There is 1 library.
[2023-10-03 16:21:28.130] [jointLog] [info] Loading pufferfish index
[2023-10-03 16:21:28.130] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 16:22:44.978] [jointLog] [info] done
[2023-10-03 16:22:45.104] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 16:23:25.069] [jointLog] [info] Number of decoys : 194
[2023-10-03 16:23:25.069] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 16:23:26.887] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 16:23:27.828] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 16:24:06.639] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 16:24:06.816] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-03 16:24:06.824] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 16:24:06.824] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-03 16:24:06.858] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-03 16:24:06.870] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-03 16:24:06.878] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-03 16:24:07.229] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-10-03 16:24:07.403] [jointLog] [info] Computed 66,657 rich equivalence classes for further processing
[2023-10-03 16:24:07.403] [jointLog] [info] Counted 1,556,019 total reads in the equivalence classes 
[2023-10-03 16:24:07.413] [jointLog] [info] Number of mappings discarded because of alignment score : 44,316,884
[2023-10-03 16:24:07.414] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 229,922
[2023-10-03 16:24:07.414] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 57,716
[2023-10-03 16:24:07.414] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 16:24:07.404] [fileLog] [info] 
At end of round 0
==================
Observed 2219319 total fragments (2219319 in most recent round)

[2023-10-03 16:24:08.546] [jointLog] [warning] Only 1556019 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 16:24:08.546] [jointLog] [info] Mapping rate = 70.1125%

[2023-10-03 16:24:08.546] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 16:24:08.547] [jointLog] [info] Starting optimizer
[2023-10-03 16:24:14.114] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 16:24:14.528] [jointLog] [info] iteration = 0 | max rel diff. = 29.3198
[2023-10-03 16:24:18.365] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 16:25:11.324] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 16:25:11.325] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 16:25:16.195] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 16:25:21.136] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 16:25:26.513] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 16:25:31.592] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 16:25:36.286] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 16:25:40.847] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 16:25:45.842] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 16:25:52.011] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 16:25:57.108] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 16:26:01.652] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 16:26:01.657] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 16:26:32.909] [jointLog] [info] iteration = 100 | max rel diff. = 1.05059
[2023-10-03 16:27:06.589] [jointLog] [info] iteration = 200 | max rel diff. = 1.91024
[2023-10-03 16:27:40.848] [jointLog] [info] iteration = 300 | max rel diff. = 0.134213
[2023-10-03 16:28:14.531] [jointLog] [info] iteration = 400 | max rel diff. = 0.127308
[2023-10-03 16:28:47.846] [jointLog] [info] iteration = 500 | max rel diff. = 0.0551216
[2023-10-03 16:29:21.095] [jointLog] [info] iteration = 600 | max rel diff. = 0.107728
[2023-10-03 16:29:53.754] [jointLog] [info] iteration = 700 | max rel diff. = 0.118449
[2023-10-03 16:30:26.320] [jointLog] [info] iteration = 800 | max rel diff. = 0.0739769
[2023-10-03 16:30:31.188] [jointLog] [info] iteration = 816 | max rel diff. = 0.00365739
[2023-10-03 16:30:33.314] [jointLog] [info] Finished optimizer
[2023-10-03 16:30:33.314] [jointLog] [info] writing output