[2022-06-15 08:59:32.295] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-06-15 08:59:32.295] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-06-15 08:59:32.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-06-15 08:59:32.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-06-15 08:59:32.295] [jointLog] [info] parsing read library format
[2022-06-15 08:59:32.295] [jointLog] [info] There is 1 library.
[2022-06-15 08:59:32.295] [jointLog] [info] Loading pufferfish index
[2022-06-15 08:59:32.295] [jointLog] [info] Loading dense pufferfish index.
[2022-06-15 09:02:49.635] [jointLog] [info] done
[2022-06-15 09:02:50.006] [jointLog] [info] Index contained 5,382,683 targets
[2022-06-15 09:04:29.613] [jointLog] [info] Number of decoys : 194
[2022-06-15 09:04:29.613] [jointLog] [info] First decoy index : 5,185,409 
[2022-06-15 09:04:34.212] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2022-06-15 09:04:37.089] [jointLog] [info] Automatically detected most likely library type as SF

[2022-06-15 09:14:08.214] [jointLog] [info] Thread saw mini-batch with a maximum of 2.04% zero probability fragments
[2022-06-15 09:14:08.259] [jointLog] [info] Thread saw mini-batch with a maximum of 2.04% zero probability fragments
[2022-06-15 09:14:08.431] [jointLog] [info] Thread saw mini-batch with a maximum of 2.04% zero probability fragments
[2022-06-15 09:14:08.901] [jointLog] [info] Thread saw mini-batch with a maximum of 2.10% zero probability fragments
[2022-06-15 09:14:09.090] [jointLog] [info] Thread saw mini-batch with a maximum of 2.12% zero probability fragments
[2022-06-15 09:14:09.235] [jointLog] [info] Thread saw mini-batch with a maximum of 1.98% zero probability fragments
[2022-06-15 09:14:09.411] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2022-06-15 09:14:09.594] [jointLog] [info] Thread saw mini-batch with a maximum of 2.08% zero probability fragments
[2022-06-15 09:14:10.155] [jointLog] [info] Computed 190,574 rich equivalence classes for further processing
[2022-06-15 09:14:10.156] [jointLog] [info] Counted 6,752,358 total reads in the equivalence classes 
[2022-06-15 09:14:10.169] [jointLog] [info] Number of mappings discarded because of alignment score : 89,964,210
[2022-06-15 09:14:10.169] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,501,955
[2022-06-15 09:14:10.169] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 409,107
[2022-06-15 09:14:10.169] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2022-06-15 09:14:10.169] [jointLog] [info] Mapping rate = 60.6364%

[2022-06-15 09:14:10.169] [jointLog] [info] finished quantifyLibrary()
[2022-06-15 09:14:10.169] [jointLog] [info] Starting optimizer
[2022-06-15 09:14:10.157] [fileLog] [info] 
At end of round 0
==================
Observed 11135814 total fragments (11135814 in most recent round)

[2022-06-15 09:14:18.793] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-06-15 09:14:19.655] [jointLog] [info] iteration = 0 | max rel diff. = 155.135
[2022-06-15 09:14:27.567] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-06-15 09:18:28.106] [jointLog] [info] Computed expected counts (for bias correction)
[2022-06-15 09:18:28.106] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-06-15 09:18:53.468] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-06-15 09:19:19.567] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-06-15 09:19:46.128] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-06-15 09:20:13.277] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-06-15 09:20:39.664] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-06-15 09:21:05.237] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-06-15 09:21:30.978] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-06-15 09:21:59.413] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-06-15 09:22:25.953] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-06-15 09:22:54.628] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-06-15 09:24:07.092] [jointLog] [info] iteration = 100 | max rel diff. = 11.0063
[2022-06-15 09:25:27.097] [jointLog] [info] iteration = 200 | max rel diff. = 5.32435
[2022-06-15 09:26:48.562] [jointLog] [info] iteration = 300 | max rel diff. = 0.276703
[2022-06-15 09:28:09.780] [jointLog] [info] iteration = 400 | max rel diff. = 1.07821
[2022-06-15 09:29:31.421] [jointLog] [info] iteration = 500 | max rel diff. = 2.07387
[2022-06-15 09:30:52.028] [jointLog] [info] iteration = 600 | max rel diff. = 0.210005
[2022-06-15 09:32:13.540] [jointLog] [info] iteration = 700 | max rel diff. = 7.57052
[2022-06-15 09:33:30.729] [jointLog] [info] iteration = 800 | max rel diff. = 0.0215746
[2022-06-15 09:34:54.871] [jointLog] [info] iteration = 900 | max rel diff. = 0.038564
[2022-06-15 09:36:13.670] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.087836
[2022-06-15 09:37:32.114] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0349405
[2022-06-15 09:37:55.629] [jointLog] [info] iteration = 1,131 | max rel diff. = 0.0064555
[2022-06-15 09:37:59.256] [jointLog] [info] Finished optimizer
[2022-06-15 09:37:59.256] [jointLog] [info] writing output