[2023-10-03 15:33:55.917] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 15:33:55.917] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 15:33:55.917] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 15:33:55.917] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 15:33:55.917] [jointLog] [info] parsing read library format
[2023-10-03 15:33:55.917] [jointLog] [info] There is 1 library.
[2023-10-03 15:33:55.918] [jointLog] [info] Loading pufferfish index
[2023-10-03 15:33:55.918] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 15:35:12.888] [jointLog] [info] done
[2023-10-03 15:35:13.064] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 15:35:54.228] [jointLog] [info] Number of decoys : 194
[2023-10-03 15:35:54.228] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 15:35:56.166] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 15:35:57.151] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 15:36:52.895] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 15:36:52.936] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-10-03 15:36:52.975] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 15:36:53.062] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 15:36:53.075] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 15:36:53.178] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-03 15:36:53.247] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 15:36:53.263] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-03 15:36:53.435] [jointLog] [info] Computed 79,137 rich equivalence classes for further processing
[2023-10-03 15:36:53.435] [jointLog] [info] Counted 2,062,120 total reads in the equivalence classes 
[2023-10-03 15:36:53.445] [jointLog] [info] Number of mappings discarded because of alignment score : 68,479,275
[2023-10-03 15:36:53.445] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 285,816
[2023-10-03 15:36:53.445] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 79,804
[2023-10-03 15:36:53.445] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 15:36:53.436] [fileLog] [info] 
At end of round 0
==================
Observed 3135500 total fragments (3135500 in most recent round)

[2023-10-03 15:36:54.843] [jointLog] [warning] Only 2062120 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 15:36:54.843] [jointLog] [info] Mapping rate = 65.7669%

[2023-10-03 15:36:54.843] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 15:36:54.843] [jointLog] [info] Starting optimizer
[2023-10-03 15:37:00.830] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 15:37:01.183] [jointLog] [info] iteration = 0 | max rel diff. = 42.8978
[2023-10-03 15:37:04.581] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 15:37:57.127] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 15:37:57.128] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 15:38:01.868] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 15:38:06.527] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 15:38:11.445] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 15:38:16.364] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 15:38:21.133] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 15:38:26.032] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 15:38:30.950] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 15:38:35.693] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 15:38:40.429] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 15:38:45.637] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 15:39:15.872] [jointLog] [info] iteration = 100 | max rel diff. = 15.1736
[2023-10-03 15:39:50.282] [jointLog] [info] iteration = 200 | max rel diff. = 0.376667
[2023-10-03 15:40:24.347] [jointLog] [info] iteration = 300 | max rel diff. = 0.0828577
[2023-10-03 15:40:58.768] [jointLog] [info] iteration = 400 | max rel diff. = 0.117451
[2023-10-03 15:41:33.257] [jointLog] [info] iteration = 500 | max rel diff. = 0.0813532
[2023-10-03 15:42:07.802] [jointLog] [info] iteration = 600 | max rel diff. = 0.0360978
[2023-10-03 15:42:41.662] [jointLog] [info] iteration = 700 | max rel diff. = 0.0222186
[2023-10-03 15:43:15.924] [jointLog] [info] iteration = 800 | max rel diff. = 0.0200155
[2023-10-03 15:43:49.880] [jointLog] [info] iteration = 900 | max rel diff. = 0.218997
[2023-10-03 15:44:05.187] [jointLog] [info] iteration = 946 | max rel diff. = 0.0019438
[2023-10-03 15:44:07.133] [jointLog] [info] Finished optimizer
[2023-10-03 15:44:07.133] [jointLog] [info] writing output