[2025-04-24 22:47:50.650] [jointLog] [info] setting maxHashResizeThreads to 8
[2025-04-24 22:47:50.650] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2025-04-24 22:47:50.656] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2025-04-24 22:47:50.656] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2025-04-24 22:47:50.656] [jointLog] [info] parsing read library format
[2025-04-24 22:47:50.665] [jointLog] [info] There is 1 library.
[2025-04-24 22:47:50.700] [jointLog] [info] Loading pufferfish index
[2025-04-24 22:47:50.701] [jointLog] [info] Loading dense pufferfish index.
[2025-04-24 22:48:07.960] [jointLog] [info] done
[2025-04-24 22:48:07.964] [jointLog] [info] Index contained 141,058 targets
[2025-04-24 22:48:07.985] [jointLog] [info] Number of decoys : 66
[2025-04-24 22:48:07.985] [jointLog] [info] First decoy index : 140,953 
[2025-04-24 22:48:08.636] [jointLog] [info] Automatically detected most likely library type as ISF
[2025-04-24 22:52:37.422] [jointLog] [info] Thread saw mini-batch with a maximum of 1.90% zero probability fragments
[2025-04-24 22:52:37.429] [jointLog] [info] Thread saw mini-batch with a maximum of 1.86% zero probability fragments
[2025-04-24 22:52:37.434] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments
[2025-04-24 22:52:37.497] [jointLog] [info] Thread saw mini-batch with a maximum of 1.80% zero probability fragments
[2025-04-24 22:52:37.521] [jointLog] [info] Thread saw mini-batch with a maximum of 1.88% zero probability fragments
[2025-04-24 22:52:37.562] [jointLog] [info] Thread saw mini-batch with a maximum of 1.86% zero probability fragments
[2025-04-24 22:52:37.644] [jointLog] [info] Thread saw mini-batch with a maximum of 1.94% zero probability fragments
[2025-04-24 22:52:37.644] [jointLog] [info] Thread saw mini-batch with a maximum of 1.86% zero probability fragments
[2025-04-24 22:52:37.755] [jointLog] [info] Computed 212,189 rich equivalence classes for further processing
[2025-04-24 22:52:37.755] [jointLog] [info] Counted 28,244,374 total reads in the equivalence classes 
[2025-04-24 22:52:37.760] [jointLog] [warning] 0.00514509% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2025-04-24 22:52:37.760] [jointLog] [info] Number of mappings discarded because of alignment score : 13,081,072
[2025-04-24 22:52:37.760] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,231,651
[2025-04-24 22:52:37.760] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,730,124
[2025-04-24 22:52:37.760] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 253,611
[2025-04-24 22:52:37.760] [jointLog] [info] Mapping rate = 80.3761%

[2025-04-24 22:52:37.760] [jointLog] [info] finished quantifyLibrary()
[2025-04-24 22:52:37.762] [jointLog] [info] Starting optimizer
[2025-04-24 22:52:37.872] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2025-04-24 22:52:37.878] [jointLog] [info] iteration = 0 | max rel diff. = 8677.81
[2025-04-24 22:52:37.755] [fileLog] [info] 
At end of round 0
==================
Observed 35140286 total fragments (35140286 in most recent round)

[2025-04-24 22:52:38.544] [jointLog] [info] iteration = 100 | max rel diff. = 19.26
[2025-04-24 22:52:39.254] [jointLog] [info] iteration = 200 | max rel diff. = 14.9067
[2025-04-24 22:52:39.906] [jointLog] [info] iteration = 300 | max rel diff. = 1.85894
[2025-04-24 22:52:40.564] [jointLog] [info] iteration = 400 | max rel diff. = 2.95392
[2025-04-24 22:52:41.347] [jointLog] [info] iteration = 500 | max rel diff. = 5.6565
[2025-04-24 22:52:42.002] [jointLog] [info] iteration = 600 | max rel diff. = 3.30986
[2025-04-24 22:52:42.658] [jointLog] [info] iteration = 700 | max rel diff. = 1.4371
[2025-04-24 22:52:43.358] [jointLog] [info] iteration = 800 | max rel diff. = 0.0697115
[2025-04-24 22:52:44.064] [jointLog] [info] iteration = 900 | max rel diff. = 0.0605035
[2025-04-24 22:52:44.728] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.157026
[2025-04-24 22:52:45.382] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.064126
[2025-04-24 22:52:46.097] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.309641
[2025-04-24 22:52:46.752] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.124849
[2025-04-24 22:52:47.407] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0769393
[2025-04-24 22:52:48.086] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0495358
[2025-04-24 22:52:48.849] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0703659
[2025-04-24 22:52:49.115] [jointLog] [info] iteration = 1,642 | max rel diff. = 0.00457495
[2025-04-24 22:52:49.119] [jointLog] [info] Finished optimizer
[2025-04-24 22:52:49.119] [jointLog] [info] writing output