[2023-09-29 22:06:18.971] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-29 22:06:18.971] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-29 22:06:18.971] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-29 22:06:18.971] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-29 22:06:18.971] [jointLog] [info] parsing read library format
[2023-09-29 22:06:18.971] [jointLog] [info] There is 1 library.
[2023-09-29 22:06:18.971] [jointLog] [info] Loading pufferfish index
[2023-09-29 22:06:18.971] [jointLog] [info] Loading dense pufferfish index.
[2023-09-29 22:07:38.901] [jointLog] [info] done
[2023-09-29 22:07:39.031] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-29 22:08:16.373] [jointLog] [info] Number of decoys : 194
[2023-09-29 22:08:16.373] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-29 22:08:18.550] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-29 22:08:20.026] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-29 22:08:47.642] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-09-29 22:08:47.687] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-29 22:08:47.766] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-09-29 22:08:47.801] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-29 22:08:47.847] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-29 22:08:48.133] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-29 22:08:48.220] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-29 22:08:48.316] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-29 22:08:48.509] [jointLog] [info] Computed 83,255 rich equivalence classes for further processing
[2023-09-29 22:08:48.509] [jointLog] [info] Counted 1,203,981 total reads in the equivalence classes 
[2023-09-29 22:08:48.518] [jointLog] [warning] 0.000316259% 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.


[2023-09-29 22:08:48.518] [jointLog] [info] Number of mappings discarded because of alignment score : 21,818,829
[2023-09-29 22:08:48.518] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 118,905
[2023-09-29 22:08:48.518] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 37,322
[2023-09-29 22:08:48.518] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-29 22:08:48.510] [fileLog] [info] 
At end of round 0
==================
Observed 1580984 total fragments (1580984 in most recent round)

[2023-09-29 22:08:49.846] [jointLog] [warning] Only 1203981 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-29 22:08:49.846] [jointLog] [info] Mapping rate = 76.1539%

[2023-09-29 22:08:49.846] [jointLog] [info] finished quantifyLibrary()
[2023-09-29 22:08:49.847] [jointLog] [info] Starting optimizer
[2023-09-29 22:08:54.477] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-29 22:08:54.810] [jointLog] [info] iteration = 0 | max rel diff. = 26.8284
[2023-09-29 22:08:58.229] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-29 22:10:00.656] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-29 22:10:00.657] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-29 22:10:06.153] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-29 22:10:11.843] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-29 22:10:17.686] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-29 22:10:23.789] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-29 22:10:29.481] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-29 22:10:34.719] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-29 22:10:40.718] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-29 22:10:46.824] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-29 22:10:52.315] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-29 22:10:58.165] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-29 22:11:28.686] [jointLog] [info] iteration = 100 | max rel diff. = 14.1064
[2023-09-29 22:12:02.505] [jointLog] [info] iteration = 200 | max rel diff. = 0.908974
[2023-09-29 22:12:36.305] [jointLog] [info] iteration = 300 | max rel diff. = 0.125587
[2023-09-29 22:13:09.862] [jointLog] [info] iteration = 400 | max rel diff. = 0.0468451
[2023-09-29 22:13:43.364] [jointLog] [info] iteration = 500 | max rel diff. = 0.159116
[2023-09-29 22:14:17.087] [jointLog] [info] iteration = 600 | max rel diff. = 0.0956195
[2023-09-29 22:14:50.477] [jointLog] [info] iteration = 700 | max rel diff. = 0.000915552
[2023-09-29 22:14:52.729] [jointLog] [info] Finished optimizer
[2023-09-29 22:14:52.729] [jointLog] [info] writing output