[2023-09-21 06:06:14.109] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 06:06:14.109] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 06:06:14.109] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 06:06:14.109] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 06:06:14.109] [jointLog] [info] parsing read library format
[2023-09-21 06:06:14.109] [jointLog] [info] There is 1 library.
[2023-09-21 06:06:14.110] [jointLog] [info] Loading pufferfish index
[2023-09-21 06:06:14.110] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 06:07:27.003] [jointLog] [info] done
[2023-09-21 06:07:27.193] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 06:08:08.980] [jointLog] [info] Number of decoys : 194
[2023-09-21 06:08:08.980] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 06:08:11.246] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 06:08:12.234] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 06:08:50.438] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-09-21 06:08:50.585] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-21 06:08:50.652] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-21 06:08:50.666] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-21 06:08:50.791] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-21 06:08:50.836] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-21 06:08:50.848] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-21 06:08:50.858] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-21 06:08:51.069] [fileLog] [info] 
At end of round 0
==================
Observed 3255209 total fragments (3255209 in most recent round)

[2023-09-21 06:08:51.068] [jointLog] [info] Computed 91,586 rich equivalence classes for further processing
[2023-09-21 06:08:51.068] [jointLog] [info] Counted 2,402,856 total reads in the equivalence classes 
[2023-09-21 06:08:51.077] [jointLog] [info] Number of mappings discarded because of alignment score : 39,233,808
[2023-09-21 06:08:51.077] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 293,219
[2023-09-21 06:08:51.077] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,914
[2023-09-21 06:08:51.077] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 06:08:52.335] [jointLog] [warning] Only 2402856 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 06:08:52.335] [jointLog] [info] Mapping rate = 73.8157%

[2023-09-21 06:08:52.335] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 06:08:52.336] [jointLog] [info] Starting optimizer
[2023-09-21 06:08:57.442] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 06:08:57.804] [jointLog] [info] iteration = 0 | max rel diff. = 48.181
[2023-09-21 06:09:01.443] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 06:09:56.422] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 06:09:56.423] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 06:10:01.596] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 06:10:06.640] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 06:10:11.775] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 06:10:16.697] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 06:10:22.011] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 06:10:27.140] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 06:10:32.096] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 06:10:36.854] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 06:10:42.169] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 06:10:46.889] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 06:11:19.358] [jointLog] [info] iteration = 100 | max rel diff. = 16.2386
[2023-09-21 06:11:56.196] [jointLog] [info] iteration = 200 | max rel diff. = 0.631708
[2023-09-21 06:12:32.551] [jointLog] [info] iteration = 300 | max rel diff. = 0.840559
[2023-09-21 06:13:09.169] [jointLog] [info] iteration = 400 | max rel diff. = 0.103707
[2023-09-21 06:13:45.964] [jointLog] [info] iteration = 500 | max rel diff. = 0.630443
[2023-09-21 06:14:22.499] [jointLog] [info] iteration = 600 | max rel diff. = 0.038682
[2023-09-21 06:14:58.848] [jointLog] [info] iteration = 700 | max rel diff. = 0.0820119
[2023-09-21 06:15:35.166] [jointLog] [info] iteration = 800 | max rel diff. = 0.0165739
[2023-09-21 06:16:11.500] [jointLog] [info] iteration = 900 | max rel diff. = 0.0375688
[2023-09-21 06:16:47.977] [jointLog] [info] iteration = 1,000 | max rel diff. = 5.37242
[2023-09-21 06:16:48.330] [jointLog] [info] iteration = 1,002 | max rel diff. = 0.00524214
[2023-09-21 06:16:50.718] [jointLog] [info] Finished optimizer
[2023-09-21 06:16:50.718] [jointLog] [info] writing output