[2021-08-10 18:31:27.675] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-10 18:31:27.675] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-10 18:31:27.675] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-10 18:31:27.675] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-10 18:31:27.675] [jointLog] [info] parsing read library format
[2021-08-10 18:31:27.675] [jointLog] [info] There is 1 library.
[2021-08-10 18:31:27.735] [jointLog] [info] Loading pufferfish index
[2021-08-10 18:31:27.735] [jointLog] [info] Loading dense pufferfish index.
[2021-08-10 18:33:07.523] [jointLog] [info] done
[2021-08-10 18:33:07.523] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-10 18:33:58.818] [jointLog] [info] Number of decoys : 194
[2021-08-10 18:33:58.818] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-10 18:33:59.779] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-10 18:34:00.272] [jointLog] [info] Automatically detected most likely library type as SF
[2021-08-10 18:34:57.485] [jointLog] [info] Thread saw mini-batch with a maximum of 2.18% zero probability fragments
[2021-08-10 18:34:57.486] [jointLog] [info] Thread saw mini-batch with a maximum of 2.34% zero probability fragments
[2021-08-10 18:34:57.500] [jointLog] [info] Thread saw mini-batch with a maximum of 2.20% zero probability fragments
[2021-08-10 18:34:57.521] [jointLog] [info] Thread saw mini-batch with a maximum of 2.36% zero probability fragments
[2021-08-10 18:34:57.570] [jointLog] [info] Thread saw mini-batch with a maximum of 2.30% zero probability fragments
[2021-08-10 18:34:57.573] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments
[2021-08-10 18:34:57.583] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments
[2021-08-10 18:34:57.639] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments
[2021-08-10 18:34:57.840] [jointLog] [info] Computed 157,935 rich equivalence classes for further processing
[2021-08-10 18:34:57.840] [jointLog] [info] Counted 14,349,624 total reads in the equivalence classes 
[2021-08-10 18:34:57.849] [jointLog] [info] Number of mappings discarded because of alignment score : 11,761,631
[2021-08-10 18:34:57.849] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 984,941
[2021-08-10 18:34:57.849] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 896,162
[2021-08-10 18:34:57.849] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-10 18:34:57.849] [jointLog] [info] Mapping rate = 79.8687%

[2021-08-10 18:34:57.849] [jointLog] [info] finished quantifyLibrary()
[2021-08-10 18:34:57.850] [jointLog] [info] Starting optimizer
[2021-08-10 18:34:57.841] [fileLog] [info] 
At end of round 0
==================
Observed 17966514 total fragments (17966514 in most recent round)

[2021-08-10 18:35:47.680] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-10 18:35:48.004] [jointLog] [info] iteration = 0 | max rel diff. = 233.47
[2021-08-10 18:35:51.324] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-10 18:37:15.536] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-10 18:37:15.537] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-10 18:37:23.727] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-10 18:37:31.797] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-10 18:37:39.473] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-10 18:37:47.190] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-10 18:37:54.612] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-10 18:38:02.573] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-10 18:38:10.359] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-10 18:38:17.965] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-10 18:38:25.913] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-10 18:38:33.668] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-10 18:38:33.670] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-10 18:39:04.250] [jointLog] [info] iteration = 100 | max rel diff. = 8.42997
[2021-08-10 18:39:37.490] [jointLog] [info] iteration = 200 | max rel diff. = 0.652268
[2021-08-10 18:40:10.386] [jointLog] [info] iteration = 300 | max rel diff. = 1.49676
[2021-08-10 18:40:42.830] [jointLog] [info] iteration = 400 | max rel diff. = 5.89585
[2021-08-10 18:41:15.219] [jointLog] [info] iteration = 500 | max rel diff. = 0.0987079
[2021-08-10 18:41:47.354] [jointLog] [info] iteration = 600 | max rel diff. = 0.426131
[2021-08-10 18:42:19.521] [jointLog] [info] iteration = 700 | max rel diff. = 0.160602
[2021-08-10 18:42:53.118] [jointLog] [info] iteration = 800 | max rel diff. = 0.104013
[2021-08-10 18:43:26.706] [jointLog] [info] iteration = 900 | max rel diff. = 2.60111
[2021-08-10 18:43:30.028] [jointLog] [info] iteration = 911 | max rel diff. = 0.00667763
[2021-08-10 18:43:31.902] [jointLog] [info] Finished optimizer
[2021-08-10 18:43:31.902] [jointLog] [info] writing output