[2023-08-27 18:14:28.784] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 18:14:28.784] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 18:14:28.784] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 18:14:28.784] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 18:14:28.784] [jointLog] [info] parsing read library format
[2023-08-27 18:14:28.784] [jointLog] [info] There is 1 library.
[2023-08-27 18:14:28.784] [jointLog] [info] Loading pufferfish index
[2023-08-27 18:14:28.784] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 18:15:47.296] [jointLog] [info] done
[2023-08-27 18:15:47.413] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 18:16:23.132] [jointLog] [info] Number of decoys : 194
[2023-08-27 18:16:23.132] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 18:16:24.547] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-27 18:16:26.247] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-27 18:24:24.594] [jointLog] [info] Thread saw mini-batch with a maximum of 8.42% zero probability fragments
[2023-08-27 18:24:24.646] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2023-08-27 18:24:24.778] [jointLog] [info] Thread saw mini-batch with a maximum of 8.80% zero probability fragments
[2023-08-27 18:24:24.991] [jointLog] [info] Thread saw mini-batch with a maximum of 8.50% zero probability fragments
[2023-08-27 18:24:25.087] [jointLog] [info] Thread saw mini-batch with a maximum of 8.40% zero probability fragments
[2023-08-27 18:24:25.311] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments
[2023-08-27 18:24:25.597] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments
[2023-08-27 18:24:25.804] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments
[2023-08-27 18:24:26.283] [jointLog] [info] Computed 366,386 rich equivalence classes for further processing
[2023-08-27 18:24:26.283] [jointLog] [info] Counted 7,142,255 total reads in the equivalence classes 
[2023-08-27 18:24:26.297] [jointLog] [info] Number of mappings discarded because of alignment score : 581,241,319
[2023-08-27 18:24:26.297] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,847,056
[2023-08-27 18:24:26.297] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 346,434
[2023-08-27 18:24:26.297] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-27 18:24:26.297] [jointLog] [info] Mapping rate = 46.0988%

[2023-08-27 18:24:26.297] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 18:24:26.297] [jointLog] [info] Starting optimizer
[2023-08-27 18:24:26.284] [fileLog] [info] 
At end of round 0
==================
Observed 15493380 total fragments (15493380 in most recent round)

[2023-08-27 18:24:31.455] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 18:24:31.809] [jointLog] [info] iteration = 0 | max rel diff. = 150.271
[2023-08-27 18:24:35.329] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 18:26:33.970] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 18:26:33.971] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 18:26:44.874] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 18:26:56.220] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 18:27:07.306] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 18:27:18.542] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 18:27:29.608] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 18:27:40.422] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 18:27:51.640] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 18:28:02.289] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 18:28:13.570] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 18:28:24.357] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 18:28:57.022] [jointLog] [info] iteration = 100 | max rel diff. = 19.9082
[2023-08-27 18:29:32.289] [jointLog] [info] iteration = 200 | max rel diff. = 3.42146
[2023-08-27 18:30:06.609] [jointLog] [info] iteration = 300 | max rel diff. = 1.38763
[2023-08-27 18:30:39.575] [jointLog] [info] iteration = 400 | max rel diff. = 0.135488
[2023-08-27 18:31:12.073] [jointLog] [info] iteration = 500 | max rel diff. = 1.29529
[2023-08-27 18:31:45.300] [jointLog] [info] iteration = 600 | max rel diff. = 0.352158
[2023-08-27 18:32:19.984] [jointLog] [info] iteration = 700 | max rel diff. = 0.194163
[2023-08-27 18:32:54.110] [jointLog] [info] iteration = 800 | max rel diff. = 0.262759
[2023-08-27 18:33:27.537] [jointLog] [info] iteration = 900 | max rel diff. = 3.02996
[2023-08-27 18:34:00.916] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.00241959
[2023-08-27 18:34:03.178] [jointLog] [info] Finished optimizer
[2023-08-27 18:34:03.178] [jointLog] [info] writing output