[2023-08-25 09:31:25.610] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 09:31:25.610] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 09:31:25.610] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 09:31:25.610] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 09:31:25.610] [jointLog] [info] parsing read library format
[2023-08-25 09:31:25.610] [jointLog] [info] There is 1 library.
[2023-08-25 09:31:25.610] [jointLog] [info] Loading pufferfish index
[2023-08-25 09:31:25.610] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 09:32:41.537] [jointLog] [info] done
[2023-08-25 09:32:41.687] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 09:33:20.847] [jointLog] [info] Number of decoys : 194
[2023-08-25 09:33:20.847] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 09:33:22.907] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 09:33:24.082] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 09:37:24.238] [jointLog] [info] Thread saw mini-batch with a maximum of 4.54% zero probability fragments
[2023-08-25 09:37:24.290] [jointLog] [info] Thread saw mini-batch with a maximum of 4.62% zero probability fragments
[2023-08-25 09:37:24.376] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-08-25 09:37:24.462] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-08-25 09:37:24.462] [jointLog] [info] Thread saw mini-batch with a maximum of 4.76% zero probability fragments
[2023-08-25 09:37:24.543] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-08-25 09:37:24.662] [jointLog] [info] Thread saw mini-batch with a maximum of 4.52% zero probability fragments
[2023-08-25 09:37:24.696] [jointLog] [info] Thread saw mini-batch with a maximum of 4.62% zero probability fragments
[2023-08-25 09:37:25.129] [fileLog] [info] 
At end of round 0
==================
Observed 13086998 total fragments (13086998 in most recent round)

[2023-08-25 09:37:25.128] [jointLog] [info] Computed 301,733 rich equivalence classes for further processing
[2023-08-25 09:37:25.128] [jointLog] [info] Counted 10,950,374 total reads in the equivalence classes 
[2023-08-25 09:37:25.140] [jointLog] [info] Number of mappings discarded because of alignment score : 127,378,502
[2023-08-25 09:37:25.140] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,242,849
[2023-08-25 09:37:25.140] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 391,878
[2023-08-25 09:37:25.140] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 09:37:25.140] [jointLog] [info] Mapping rate = 83.6737%

[2023-08-25 09:37:25.140] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 09:37:25.141] [jointLog] [info] Starting optimizer
[2023-08-25 09:37:30.059] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 09:37:30.423] [jointLog] [info] iteration = 0 | max rel diff. = 219.105
[2023-08-25 09:37:33.800] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 09:39:17.156] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 09:39:17.156] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 09:39:26.640] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 09:39:35.861] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 09:39:45.546] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 09:39:54.675] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 09:40:04.157] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 09:40:13.648] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 09:40:22.710] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 09:40:31.672] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 09:40:41.163] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 09:40:50.685] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 09:40:50.691] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 09:41:20.827] [jointLog] [info] iteration = 100 | max rel diff. = 7.35113
[2023-08-25 09:41:54.059] [jointLog] [info] iteration = 200 | max rel diff. = 1.98282
[2023-08-25 09:42:28.210] [jointLog] [info] iteration = 300 | max rel diff. = 2.50064
[2023-08-25 09:43:01.705] [jointLog] [info] iteration = 400 | max rel diff. = 2.30584
[2023-08-25 09:43:34.813] [jointLog] [info] iteration = 500 | max rel diff. = 0.224432
[2023-08-25 09:44:09.059] [jointLog] [info] iteration = 600 | max rel diff. = 0.215163
[2023-08-25 09:44:42.823] [jointLog] [info] iteration = 700 | max rel diff. = 0.0556849
[2023-08-25 09:45:16.648] [jointLog] [info] iteration = 800 | max rel diff. = 0.231272
[2023-08-25 09:45:50.236] [jointLog] [info] iteration = 900 | max rel diff. = 0.0361346
[2023-08-25 09:46:24.021] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0181559
[2023-08-25 09:46:57.004] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.225777
[2023-08-25 09:47:29.231] [jointLog] [info] iteration = 1,197 | max rel diff. = 0.00412767
[2023-08-25 09:47:31.047] [jointLog] [info] Finished optimizer
[2023-08-25 09:47:31.047] [jointLog] [info] writing output