[2023-09-24 19:36:16.296] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 19:36:16.296] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 19:36:16.296] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 19:36:16.296] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 19:36:16.296] [jointLog] [info] parsing read library format
[2023-09-24 19:36:16.296] [jointLog] [info] There is 1 library.
[2023-09-24 19:36:16.296] [jointLog] [info] Loading pufferfish index
[2023-09-24 19:36:16.297] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 19:37:30.272] [jointLog] [info] done
[2023-09-24 19:37:30.396] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 19:38:05.497] [jointLog] [info] Number of decoys : 194
[2023-09-24 19:38:05.497] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 19:38:06.492] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 19:38:07.648] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 19:38:45.351] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-09-24 19:38:45.470] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-24 19:38:45.482] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-24 19:38:45.536] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-24 19:38:45.709] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-24 19:38:45.789] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-24 19:38:45.799] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-24 19:38:45.981] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-24 19:38:46.159] [jointLog] [info] Computed 72,796 rich equivalence classes for further processing
[2023-09-24 19:38:46.159] [jointLog] [info] Counted 1,856,182 total reads in the equivalence classes 
[2023-09-24 19:38:46.165] [jointLog] [info] Number of mappings discarded because of alignment score : 54,641,927
[2023-09-24 19:38:46.165] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 253,086
[2023-09-24 19:38:46.165] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,092
[2023-09-24 19:38:46.165] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 19:38:46.159] [fileLog] [info] 
At end of round 0
==================
Observed 2591621 total fragments (2591621 in most recent round)

[2023-09-24 19:38:47.064] [jointLog] [warning] Only 1856182 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 19:38:47.064] [jointLog] [info] Mapping rate = 71.6224%

[2023-09-24 19:38:47.064] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 19:38:47.064] [jointLog] [info] Starting optimizer
[2023-09-24 19:38:50.476] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 19:38:50.804] [jointLog] [info] iteration = 0 | max rel diff. = 45.3117
[2023-09-24 19:38:54.002] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 19:39:44.206] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 19:39:44.206] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 19:39:48.710] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 19:39:53.180] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 19:39:58.086] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 19:40:02.363] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 19:40:06.986] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 19:40:11.647] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 19:40:16.016] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 19:40:20.722] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 19:40:25.303] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 19:40:30.527] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 19:41:00.028] [jointLog] [info] iteration = 100 | max rel diff. = 13.1984
[2023-09-24 19:41:32.801] [jointLog] [info] iteration = 200 | max rel diff. = 0.261617
[2023-09-24 19:42:05.466] [jointLog] [info] iteration = 300 | max rel diff. = 0.211744
[2023-09-24 19:42:38.244] [jointLog] [info] iteration = 400 | max rel diff. = 0.246036
[2023-09-24 19:43:11.102] [jointLog] [info] iteration = 500 | max rel diff. = 0.0154866
[2023-09-24 19:43:43.819] [jointLog] [info] iteration = 600 | max rel diff. = 6.56033
[2023-09-24 19:44:16.161] [jointLog] [info] iteration = 700 | max rel diff. = 0.0324472
[2023-09-24 19:44:48.169] [jointLog] [info] iteration = 800 | max rel diff. = 0.264739
[2023-09-24 19:45:20.003] [jointLog] [info] iteration = 900 | max rel diff. = 0.0351863
[2023-09-24 19:45:29.583] [jointLog] [info] iteration = 931 | max rel diff. = 0.00680904
[2023-09-24 19:45:31.480] [jointLog] [info] Finished optimizer
[2023-09-24 19:45:31.480] [jointLog] [info] writing output