[2023-08-27 20:26:38.214] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 20:26:38.214] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 20:26:38.214] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 20:26:38.214] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 20:26:38.214] [jointLog] [info] parsing read library format
[2023-08-27 20:26:38.214] [jointLog] [info] There is 1 library.
[2023-08-27 20:26:38.215] [jointLog] [info] Loading pufferfish index
[2023-08-27 20:26:38.215] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 20:27:48.610] [jointLog] [info] done
[2023-08-27 20:27:48.734] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 20:28:24.863] [jointLog] [info] Number of decoys : 194
[2023-08-27 20:28:24.863] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 20:28:26.071] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-27 20:28:26.857] [jointLog] [info] Automatically detected most likely library type as U

[2023-08-27 20:32:34.368] [fileLog] [info] 
At end of round 0
==================
Observed 31609417 total fragments (31609417 in most recent round)

[2023-08-27 20:32:34.367] [jointLog] [info] Computed 668,311 rich equivalence classes for further processing
[2023-08-27 20:32:34.367] [jointLog] [info] Counted 29,710,298 total reads in the equivalence classes 
[2023-08-27 20:32:34.374] [jointLog] [info] Number of mappings discarded because of alignment score : 40,928,158
[2023-08-27 20:32:34.374] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,069,734
[2023-08-27 20:32:34.374] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 723,308
[2023-08-27 20:32:34.374] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-27 20:32:34.374] [jointLog] [info] Mapping rate = 93.9919%

[2023-08-27 20:32:34.374] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 20:32:34.375] [jointLog] [info] Starting optimizer
[2023-08-27 20:32:38.451] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 20:32:38.800] [jointLog] [info] iteration = 0 | max rel diff. = 608.31
[2023-08-27 20:32:42.295] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 20:35:02.280] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 20:35:02.280] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 20:35:14.917] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 20:35:27.721] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 20:35:40.380] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 20:35:53.429] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 20:36:05.868] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 20:36:18.764] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 20:36:31.337] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 20:36:43.480] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 20:36:55.777] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 20:37:08.526] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 20:37:08.528] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 20:37:40.663] [jointLog] [info] iteration = 100 | max rel diff. = 18.8311
[2023-08-27 20:38:15.570] [jointLog] [info] iteration = 200 | max rel diff. = 13.9806
[2023-08-27 20:38:50.911] [jointLog] [info] iteration = 300 | max rel diff. = 4.31238
[2023-08-27 20:39:25.787] [jointLog] [info] iteration = 400 | max rel diff. = 5.36307
[2023-08-27 20:40:00.817] [jointLog] [info] iteration = 500 | max rel diff. = 0.730927
[2023-08-27 20:40:35.837] [jointLog] [info] iteration = 600 | max rel diff. = 0.653061
[2023-08-27 20:41:10.909] [jointLog] [info] iteration = 700 | max rel diff. = 0.930335
[2023-08-27 20:41:45.922] [jointLog] [info] iteration = 800 | max rel diff. = 1.10679
[2023-08-27 20:42:21.033] [jointLog] [info] iteration = 900 | max rel diff. = 1.32449
[2023-08-27 20:42:55.939] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.451625
[2023-08-27 20:43:30.723] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.175611
[2023-08-27 20:43:54.648] [jointLog] [info] iteration = 1,170 | max rel diff. = 0.00720865
[2023-08-27 20:43:56.446] [jointLog] [info] Finished optimizer
[2023-08-27 20:43:56.446] [jointLog] [info] writing output