[2021-08-11 13:25:12.916] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-11 13:25:12.916] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-11 13:25:12.916] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-11 13:25:12.916] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-11 13:25:12.916] [jointLog] [info] parsing read library format
[2021-08-11 13:25:12.916] [jointLog] [info] There is 1 library.
[2021-08-11 13:25:12.977] [jointLog] [info] Loading pufferfish index
[2021-08-11 13:25:12.977] [jointLog] [info] Loading dense pufferfish index.
[2021-08-11 13:26:57.816] [jointLog] [info] done
[2021-08-11 13:26:57.816] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-11 13:27:51.046] [jointLog] [info] Number of decoys : 194
[2021-08-11 13:27:51.046] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-11 13:27:52.875] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-11 13:27:53.520] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-11 13:28:40.168] [jointLog] [info] Thread saw mini-batch with a maximum of 5.04% zero probability fragments
[2021-08-11 13:28:40.287] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2021-08-11 13:28:40.290] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2021-08-11 13:28:40.328] [jointLog] [info] Thread saw mini-batch with a maximum of 5.00% zero probability fragments
[2021-08-11 13:28:40.337] [jointLog] [info] Thread saw mini-batch with a maximum of 4.86% zero probability fragments
[2021-08-11 13:28:40.348] [jointLog] [info] Thread saw mini-batch with a maximum of 5.06% zero probability fragments
[2021-08-11 13:28:40.378] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2021-08-11 13:28:40.410] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments
[2021-08-11 13:28:40.596] [jointLog] [info] Computed 223,858 rich equivalence classes for further processing
[2021-08-11 13:28:40.596] [jointLog] [info] Counted 5,849,587 total reads in the equivalence classes 
[2021-08-11 13:28:40.607] [jointLog] [info] Number of mappings discarded because of alignment score : 10,301,775
[2021-08-11 13:28:40.607] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 152,370
[2021-08-11 13:28:40.607] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 95,728
[2021-08-11 13:28:40.607] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-11 13:28:40.607] [jointLog] [info] Mapping rate = 91.283%

[2021-08-11 13:28:40.607] [jointLog] [info] finished quantifyLibrary()
[2021-08-11 13:28:40.607] [jointLog] [info] Starting optimizer
[2021-08-11 13:28:40.597] [fileLog] [info] 
At end of round 0
==================
Observed 6408192 total fragments (6408192 in most recent round)

[2021-08-11 13:28:44.760] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-11 13:28:45.088] [jointLog] [info] iteration = 0 | max rel diff. = 105.348
[2021-08-11 13:28:48.410] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-11 13:30:36.920] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-11 13:30:36.920] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-11 13:30:46.438] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-11 13:30:56.431] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-11 13:31:06.874] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-11 13:31:16.976] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-11 13:31:26.954] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-11 13:31:36.397] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-11 13:31:46.493] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-11 13:31:56.543] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-11 13:32:06.530] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-11 13:32:16.120] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-11 13:32:45.990] [jointLog] [info] iteration = 100 | max rel diff. = 11.0732
[2021-08-11 13:33:19.978] [jointLog] [info] iteration = 200 | max rel diff. = 8.37306
[2021-08-11 13:33:54.834] [jointLog] [info] iteration = 300 | max rel diff. = 1.84482
[2021-08-11 13:34:29.599] [jointLog] [info] iteration = 400 | max rel diff. = 0.824215
[2021-08-11 13:35:04.137] [jointLog] [info] iteration = 500 | max rel diff. = 6.26992
[2021-08-11 13:35:37.704] [jointLog] [info] iteration = 600 | max rel diff. = 5.71675
[2021-08-11 13:36:12.283] [jointLog] [info] iteration = 700 | max rel diff. = 0.318105
[2021-08-11 13:36:45.976] [jointLog] [info] iteration = 800 | max rel diff. = 5.14356
[2021-08-11 13:37:20.312] [jointLog] [info] iteration = 900 | max rel diff. = 0.0866564
[2021-08-11 13:37:54.430] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.027111
[2021-08-11 13:38:28.834] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.385
[2021-08-11 13:38:45.073] [jointLog] [info] iteration = 1,149 | max rel diff. = 0.00794211
[2021-08-11 13:38:47.020] [jointLog] [info] Finished optimizer
[2021-08-11 13:38:47.020] [jointLog] [info] writing output