[2021-03-27 04:38:52.153] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-27 04:38:52.153] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-27 04:38:52.153] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-27 04:38:52.153] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-27 04:38:52.153] [jointLog] [info] parsing read library format
[2021-03-27 04:38:52.154] [jointLog] [info] There is 1 library.
[2021-03-27 04:38:52.313] [jointLog] [info] Loading pufferfish index
[2021-03-27 04:38:52.313] [jointLog] [info] Loading dense pufferfish index.
[2021-03-27 04:40:37.650] [jointLog] [info] done
[2021-03-27 04:40:37.650] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-27 04:41:28.862] [jointLog] [info] Number of decoys : 194
[2021-03-27 04:41:28.862] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-27 04:41:29.924] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-27 04:41:30.419] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-27 04:42:42.071] [jointLog] [info] Computed 195,014 rich equivalence classes for further processing
[2021-03-27 04:42:42.071] [jointLog] [info] Counted 9,365,821 total reads in the equivalence classes 
[2021-03-27 04:42:42.079] [jointLog] [info] Number of mappings discarded because of alignment score : 4,546,585
[2021-03-27 04:42:42.079] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 136,681
[2021-03-27 04:42:42.079] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 122,516
[2021-03-27 04:42:42.079] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-27 04:42:42.079] [jointLog] [info] Mapping rate = 97.6317%

[2021-03-27 04:42:42.079] [jointLog] [info] finished quantifyLibrary()
[2021-03-27 04:42:42.079] [jointLog] [info] Starting optimizer
[2021-03-27 04:42:42.072] [fileLog] [info] 
At end of round 0
==================
Observed 9593009 total fragments (9593009 in most recent round)

[2021-03-27 04:42:46.571] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-27 04:42:46.902] [jointLog] [info] iteration = 0 | max rel diff. = 195.804
[2021-03-27 04:42:50.220] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-27 04:44:24.548] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-27 04:44:24.548] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-27 04:44:32.755] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-27 04:44:41.622] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-27 04:44:50.759] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-27 04:44:59.851] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-27 04:45:08.675] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-27 04:45:17.528] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-27 04:45:26.226] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-27 04:45:35.028] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-27 04:45:43.789] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-27 04:45:52.962] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-27 04:46:23.633] [jointLog] [info] iteration = 100 | max rel diff. = 14.7096
[2021-03-27 04:46:57.257] [jointLog] [info] iteration = 200 | max rel diff. = 17.3731
[2021-03-27 04:47:30.818] [jointLog] [info] iteration = 300 | max rel diff. = 1.33868
[2021-03-27 04:48:04.475] [jointLog] [info] iteration = 400 | max rel diff. = 0.738608
[2021-03-27 04:48:38.118] [jointLog] [info] iteration = 500 | max rel diff. = 0.633934
[2021-03-27 04:49:11.808] [jointLog] [info] iteration = 600 | max rel diff. = 0.24414
[2021-03-27 04:49:45.476] [jointLog] [info] iteration = 700 | max rel diff. = 2.20116
[2021-03-27 04:50:19.197] [jointLog] [info] iteration = 800 | max rel diff. = 0.0553137
[2021-03-27 04:50:52.795] [jointLog] [info] iteration = 900 | max rel diff. = 0.076796
[2021-03-27 04:51:26.492] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0659639
[2021-03-27 04:52:00.101] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.265134
[2021-03-27 04:52:33.801] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0661575
[2021-03-27 04:52:59.025] [jointLog] [info] iteration = 1,276 | max rel diff. = 0.00850608
[2021-03-27 04:53:01.091] [jointLog] [info] Finished optimizer
[2021-03-27 04:53:01.091] [jointLog] [info] writing output