[2023-08-30 15:25:58.653] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-30 15:25:58.653] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-30 15:25:58.653] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-30 15:25:58.653] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-30 15:25:58.653] [jointLog] [info] parsing read library format
[2023-08-30 15:25:58.653] [jointLog] [info] There is 1 library.
[2023-08-30 15:25:58.653] [jointLog] [info] Loading pufferfish index
[2023-08-30 15:25:58.654] [jointLog] [info] Loading dense pufferfish index.
[2023-08-30 15:28:18.535] [jointLog] [info] done
[2023-08-30 15:28:18.820] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-30 15:29:25.913] [jointLog] [info] Number of decoys : 194
[2023-08-30 15:29:25.913] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-30 15:29:28.918] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-30 15:29:29.928] [jointLog] [info] Automatically detected most likely library type as U

[2023-08-30 15:30:59.024] [jointLog] [info] Computed 44,522 rich equivalence classes for further processing
[2023-08-30 15:30:59.024] [jointLog] [info] Counted 7,584,029 total reads in the equivalence classes 
[2023-08-30 15:30:59.057] [jointLog] [warning] 0.433328% 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 25.


[2023-08-30 15:30:59.057] [jointLog] [info] Number of mappings discarded because of alignment score : 5,976,930
[2023-08-30 15:30:59.057] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 164,708
[2023-08-30 15:30:59.057] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 16,903
[2023-08-30 15:30:59.057] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-30 15:30:59.057] [jointLog] [info] Mapping rate = 95.9132%

[2023-08-30 15:30:59.057] [jointLog] [info] finished quantifyLibrary()
[2023-08-30 15:30:59.059] [jointLog] [info] Starting optimizer
[2023-08-30 15:30:59.032] [fileLog] [info] 
At end of round 0
==================
Observed 7907183 total fragments (7907183 in most recent round)

[2023-08-30 15:31:06.984] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-30 15:31:07.421] [jointLog] [info] iteration = 0 | max rel diff. = 325.419
[2023-08-30 15:31:13.366] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-30 15:31:52.445] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-30 15:31:52.446] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-30 15:31:57.069] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-30 15:32:02.188] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-30 15:32:06.727] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-30 15:32:11.718] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-30 15:32:16.257] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-30 15:32:20.558] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-30 15:32:25.162] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-30 15:32:29.760] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-30 15:32:34.815] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-30 15:32:39.625] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 15:33:33.154] [jointLog] [info] iteration = 100 | max rel diff. = 12.5162
[2023-08-30 15:34:30.758] [jointLog] [info] iteration = 200 | max rel diff. = 5.72274
[2023-08-30 15:35:32.753] [jointLog] [info] iteration = 300 | max rel diff. = 1.90344
[2023-08-30 15:36:31.462] [jointLog] [info] iteration = 400 | max rel diff. = 17.7897
[2023-08-30 15:37:24.691] [jointLog] [info] iteration = 500 | max rel diff. = 1.7976
[2023-08-30 15:38:21.170] [jointLog] [info] iteration = 600 | max rel diff. = 0.438625
[2023-08-30 15:39:20.230] [jointLog] [info] iteration = 700 | max rel diff. = 1.32497
[2023-08-30 15:40:15.688] [jointLog] [info] iteration = 800 | max rel diff. = 0.738251
[2023-08-30 15:41:11.276] [jointLog] [info] iteration = 900 | max rel diff. = 0.0449161
[2023-08-30 15:42:06.641] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0933882
[2023-08-30 15:43:01.561] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0931179
[2023-08-30 15:43:42.387] [jointLog] [info] iteration = 1,176 | max rel diff. = 0.0065375
[2023-08-30 15:43:45.646] [jointLog] [info] Finished optimizer
[2023-08-30 15:43:45.646] [jointLog] [info] writing output