[2021-03-29 13:17:32.921] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-29 13:17:32.921] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-29 13:17:32.921] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-29 13:17:32.921] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-29 13:17:32.921] [jointLog] [info] parsing read library format
[2021-03-29 13:17:32.921] [jointLog] [info] There is 1 library.
[2021-03-29 13:17:33.037] [jointLog] [info] Loading pufferfish index
[2021-03-29 13:17:33.037] [jointLog] [info] Loading dense pufferfish index.
[2021-03-29 13:19:20.923] [jointLog] [info] done
[2021-03-29 13:19:20.923] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-29 13:20:15.793] [jointLog] [info] Number of decoys : 194
[2021-03-29 13:20:15.793] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-29 13:20:17.461] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-29 13:20:17.793] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-29 13:21:39.135] [fileLog] [info] 
At end of round 0
==================
Observed 12760482 total fragments (12760482 in most recent round)

[2021-03-29 13:21:39.134] [jointLog] [info] Computed 383,813 rich equivalence classes for further processing
[2021-03-29 13:21:39.134] [jointLog] [info] Counted 12,343,692 total reads in the equivalence classes 
[2021-03-29 13:21:39.146] [jointLog] [info] Number of mappings discarded because of alignment score : 6,364,209
[2021-03-29 13:21:39.146] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 228,684
[2021-03-29 13:21:39.146] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 198,555
[2021-03-29 13:21:39.146] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-29 13:21:39.146] [jointLog] [info] Mapping rate = 96.7337%

[2021-03-29 13:21:39.146] [jointLog] [info] finished quantifyLibrary()
[2021-03-29 13:21:39.147] [jointLog] [info] Starting optimizer
[2021-03-29 13:21:43.714] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-29 13:21:44.061] [jointLog] [info] iteration = 0 | max rel diff. = 193.785
[2021-03-29 13:21:47.513] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-29 13:23:39.276] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-29 13:23:39.276] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-29 13:23:49.280] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-29 13:23:59.354] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-29 13:24:09.644] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-29 13:24:20.611] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-29 13:24:31.035] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-29 13:24:41.624] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-29 13:24:51.790] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-29 13:25:02.015] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-29 13:25:12.167] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-29 13:25:22.283] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-29 13:25:53.839] [jointLog] [info] iteration = 100 | max rel diff. = 17.9275
[2021-03-29 13:26:28.382] [jointLog] [info] iteration = 200 | max rel diff. = 7.49069
[2021-03-29 13:27:02.721] [jointLog] [info] iteration = 300 | max rel diff. = 11.7705
[2021-03-29 13:27:36.987] [jointLog] [info] iteration = 400 | max rel diff. = 9.14156
[2021-03-29 13:28:11.417] [jointLog] [info] iteration = 500 | max rel diff. = 0.337943
[2021-03-29 13:28:45.675] [jointLog] [info] iteration = 600 | max rel diff. = 0.179096
[2021-03-29 13:29:19.659] [jointLog] [info] iteration = 700 | max rel diff. = 0.141687
[2021-03-29 13:29:53.617] [jointLog] [info] iteration = 800 | max rel diff. = 0.0361191
[2021-03-29 13:30:27.728] [jointLog] [info] iteration = 900 | max rel diff. = 3.45853
[2021-03-29 13:31:01.715] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.210254
[2021-03-29 13:31:35.828] [jointLog] [info] iteration = 1,100 | max rel diff. = 5.82029
[2021-03-29 13:32:09.747] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0968926
[2021-03-29 13:32:43.830] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0466898
[2021-03-29 13:32:48.249] [jointLog] [info] iteration = 1,314 | max rel diff. = 0.00502636
[2021-03-29 13:32:50.117] [jointLog] [info] Finished optimizer
[2021-03-29 13:32:50.117] [jointLog] [info] writing output