[2023-08-25 12:22:21.393] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 12:22:21.394] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 12:22:21.394] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 12:22:21.394] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 12:22:21.394] [jointLog] [info] parsing read library format
[2023-08-25 12:22:21.394] [jointLog] [info] There is 1 library.
[2023-08-25 12:22:21.394] [jointLog] [info] Loading pufferfish index
[2023-08-25 12:22:21.394] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 12:23:42.448] [jointLog] [info] done
[2023-08-25 12:23:42.574] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 12:24:20.036] [jointLog] [info] Number of decoys : 194
[2023-08-25 12:24:20.036] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 12:24:22.111] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 12:24:23.636] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 12:31:13.086] [jointLog] [info] Thread saw mini-batch with a maximum of 4.74% zero probability fragments
[2023-08-25 12:31:13.128] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-08-25 12:31:13.181] [jointLog] [info] Thread saw mini-batch with a maximum of 4.74% zero probability fragments
[2023-08-25 12:31:13.273] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-08-25 12:31:13.287] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-08-25 12:31:13.463] [jointLog] [info] Thread saw mini-batch with a maximum of 4.44% zero probability fragments
[2023-08-25 12:31:13.502] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-08-25 12:31:13.703] [jointLog] [info] Thread saw mini-batch with a maximum of 4.62% zero probability fragments
[2023-08-25 12:31:14.092] [fileLog] [info] 
At end of round 0
==================
Observed 22051728 total fragments (22051728 in most recent round)

[2023-08-25 12:31:14.091] [jointLog] [info] Computed 342,958 rich equivalence classes for further processing
[2023-08-25 12:31:14.091] [jointLog] [info] Counted 16,760,141 total reads in the equivalence classes 
[2023-08-25 12:31:14.098] [jointLog] [info] Number of mappings discarded because of alignment score : 352,442,976
[2023-08-25 12:31:14.098] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,452,243
[2023-08-25 12:31:14.098] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 768,541
[2023-08-25 12:31:14.098] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 12:31:14.098] [jointLog] [info] Mapping rate = 76.0038%

[2023-08-25 12:31:14.098] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 12:31:14.099] [jointLog] [info] Starting optimizer
[2023-08-25 12:31:17.863] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 12:31:18.202] [jointLog] [info] iteration = 0 | max rel diff. = 408.381
[2023-08-25 12:31:21.563] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 12:33:18.406] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 12:33:18.406] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 12:33:28.754] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 12:33:39.389] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 12:33:50.293] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 12:34:00.931] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 12:34:11.791] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 12:34:22.483] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 12:34:32.833] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 12:34:43.451] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 12:34:54.046] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 12:35:04.572] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 12:35:34.466] [jointLog] [info] iteration = 100 | max rel diff. = 7.15478
[2023-08-25 12:36:07.639] [jointLog] [info] iteration = 200 | max rel diff. = 3.47247
[2023-08-25 12:36:41.398] [jointLog] [info] iteration = 300 | max rel diff. = 1.60126
[2023-08-25 12:37:15.423] [jointLog] [info] iteration = 400 | max rel diff. = 0.211461
[2023-08-25 12:37:49.455] [jointLog] [info] iteration = 500 | max rel diff. = 0.195309
[2023-08-25 12:38:23.460] [jointLog] [info] iteration = 600 | max rel diff. = 0.127647
[2023-08-25 12:38:58.379] [jointLog] [info] iteration = 700 | max rel diff. = 0.41071
[2023-08-25 12:39:33.603] [jointLog] [info] iteration = 800 | max rel diff. = 0.0628111
[2023-08-25 12:40:07.215] [jointLog] [info] iteration = 900 | max rel diff. = 0.0151178
[2023-08-25 12:40:40.740] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0298426
[2023-08-25 12:41:14.706] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.07798
[2023-08-25 12:41:46.824] [jointLog] [info] iteration = 1,197 | max rel diff. = 0.00670537
[2023-08-25 12:41:48.429] [jointLog] [info] Finished optimizer
[2023-08-25 12:41:48.429] [jointLog] [info] writing output