[2023-09-20 08:33:45.287] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 08:33:45.287] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 08:33:45.287] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 08:33:45.287] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 08:33:45.287] [jointLog] [info] parsing read library format
[2023-09-20 08:33:45.288] [jointLog] [info] There is 1 library.
[2023-09-20 08:33:45.288] [jointLog] [info] Loading pufferfish index
[2023-09-20 08:33:45.288] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 08:35:05.105] [jointLog] [info] done
[2023-09-20 08:35:05.282] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 08:35:46.150] [jointLog] [info] Number of decoys : 194
[2023-09-20 08:35:46.150] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 08:35:48.420] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 08:35:49.519] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 08:36:14.900] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-09-20 08:36:14.905] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-09-20 08:36:14.913] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-20 08:36:14.972] [jointLog] [info] Thread saw mini-batch with a maximum of 3.23% zero probability fragments
[2023-09-20 08:36:15.034] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-20 08:36:15.104] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-09-20 08:36:15.132] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-20 08:36:15.268] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-20 08:36:15.488] [jointLog] [info] Computed 66,808 rich equivalence classes for further processing
[2023-09-20 08:36:15.488] [jointLog] [info] Counted 1,572,319 total reads in the equivalence classes 
[2023-09-20 08:36:15.489] [fileLog] [info] 
At end of round 0
==================
Observed 2046144 total fragments (2046144 in most recent round)

[2023-09-20 08:36:15.516] [jointLog] [info] Number of mappings discarded because of alignment score : 28,241,893
[2023-09-20 08:36:15.516] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 182,982
[2023-09-20 08:36:15.516] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 44,237
[2023-09-20 08:36:15.516] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 08:36:17.112] [jointLog] [warning] Only 1572319 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 08:36:17.112] [jointLog] [info] Mapping rate = 76.843%

[2023-09-20 08:36:17.112] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 08:36:17.112] [jointLog] [info] Starting optimizer
[2023-09-20 08:36:22.995] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 08:36:23.349] [jointLog] [info] iteration = 0 | max rel diff. = 34.8238
[2023-09-20 08:36:26.916] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 08:37:08.548] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 08:37:08.548] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 08:37:12.639] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 08:37:16.425] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 08:37:20.482] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 08:37:24.341] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 08:37:28.134] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 08:37:32.108] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 08:37:36.119] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 08:37:39.986] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 08:37:43.652] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 08:37:47.534] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 08:38:21.024] [jointLog] [info] iteration = 100 | max rel diff. = 3.62261
[2023-09-20 08:38:57.846] [jointLog] [info] iteration = 200 | max rel diff. = 0.200168
[2023-09-20 08:39:34.477] [jointLog] [info] iteration = 300 | max rel diff. = 0.0281635
[2023-09-20 08:40:11.000] [jointLog] [info] iteration = 400 | max rel diff. = 1.06798
[2023-09-20 08:40:47.786] [jointLog] [info] iteration = 500 | max rel diff. = 0.0783469
[2023-09-20 08:41:24.702] [jointLog] [info] iteration = 600 | max rel diff. = 0.0316474
[2023-09-20 08:42:01.749] [jointLog] [info] iteration = 700 | max rel diff. = 0.0171039
[2023-09-20 08:42:38.596] [jointLog] [info] iteration = 800 | max rel diff. = 0.0294433
[2023-09-20 08:42:52.871] [jointLog] [info] iteration = 839 | max rel diff. = 0.000376272
[2023-09-20 08:42:55.546] [jointLog] [info] Finished optimizer
[2023-09-20 08:42:55.546] [jointLog] [info] writing output