[2025-04-24 22:47:53.818] [jointLog] [info] setting maxHashResizeThreads to 8
[2025-04-24 22:47:53.818] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2025-04-24 22:47:53.823] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2025-04-24 22:47:53.823] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2025-04-24 22:47:53.823] [jointLog] [info] parsing read library format
[2025-04-24 22:47:53.834] [jointLog] [info] There is 1 library.
[2025-04-24 22:47:53.865] [jointLog] [info] Loading pufferfish index
[2025-04-24 22:47:53.865] [jointLog] [info] Loading dense pufferfish index.
[2025-04-24 22:48:10.217] [jointLog] [info] done
[2025-04-24 22:48:10.226] [jointLog] [info] Index contained 141,058 targets
[2025-04-24 22:48:10.246] [jointLog] [info] Number of decoys : 66
[2025-04-24 22:48:10.246] [jointLog] [info] First decoy index : 140,953 
[2025-04-24 22:48:10.752] [jointLog] [info] Automatically detected most likely library type as ISF
[2025-04-24 22:50:33.729] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2025-04-24 22:50:33.741] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments
[2025-04-24 22:50:33.760] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2025-04-24 22:50:33.790] [jointLog] [info] Thread saw mini-batch with a maximum of 1.96% zero probability fragments
[2025-04-24 22:50:33.866] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2025-04-24 22:50:33.919] [jointLog] [info] Thread saw mini-batch with a maximum of 1.98% zero probability fragments
[2025-04-24 22:50:33.934] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2025-04-24 22:50:33.960] [jointLog] [info] Thread saw mini-batch with a maximum of 2.08% zero probability fragments
[2025-04-24 22:50:34.049] [jointLog] [info] Computed 203,510 rich equivalence classes for further processing
[2025-04-24 22:50:34.049] [jointLog] [info] Counted 16,843,875 total reads in the equivalence classes 
[2025-04-24 22:50:34.055] [jointLog] [warning] 0.00291104% 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 22:50:34.055] [jointLog] [info] Number of mappings discarded because of alignment score : 7,788,384
[2025-04-24 22:50:34.055] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,367,535
[2025-04-24 22:50:34.055] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,122,366
[2025-04-24 22:50:34.055] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 155,850
[2025-04-24 22:50:34.055] [jointLog] [info] Mapping rate = 79.2137%

[2025-04-24 22:50:34.055] [jointLog] [info] finished quantifyLibrary()
[2025-04-24 22:50:34.056] [jointLog] [info] Starting optimizer
[2025-04-24 22:50:34.140] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2025-04-24 22:50:34.148] [jointLog] [info] iteration = 0 | max rel diff. = 7848.13
[2025-04-24 22:50:34.050] [fileLog] [info] 
At end of round 0
==================
Observed 21263852 total fragments (21263852 in most recent round)

[2025-04-24 22:50:34.781] [jointLog] [info] iteration = 100 | max rel diff. = 18.3035
[2025-04-24 22:50:35.405] [jointLog] [info] iteration = 200 | max rel diff. = 18.9308
[2025-04-24 22:50:36.030] [jointLog] [info] iteration = 300 | max rel diff. = 3.18906
[2025-04-24 22:50:36.657] [jointLog] [info] iteration = 400 | max rel diff. = 8.29865
[2025-04-24 22:50:37.282] [jointLog] [info] iteration = 500 | max rel diff. = 2.40346
[2025-04-24 22:50:37.906] [jointLog] [info] iteration = 600 | max rel diff. = 4.99775
[2025-04-24 22:50:38.529] [jointLog] [info] iteration = 700 | max rel diff. = 0.116439
[2025-04-24 22:50:39.149] [jointLog] [info] iteration = 800 | max rel diff. = 0.112
[2025-04-24 22:50:39.769] [jointLog] [info] iteration = 900 | max rel diff. = 0.150346
[2025-04-24 22:50:40.390] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.16346
[2025-04-24 22:50:41.008] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.201575
[2025-04-24 22:50:41.629] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.100198
[2025-04-24 22:50:42.251] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.101934
[2025-04-24 22:50:42.792] [jointLog] [info] iteration = 1,388 | max rel diff. = 0.00506158
[2025-04-24 22:50:42.795] [jointLog] [info] Finished optimizer
[2025-04-24 22:50:42.795] [jointLog] [info] writing output