[2021-03-23 13:12:22.720] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-23 13:12:22.720] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-23 13:12:22.720] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-23 13:12:22.720] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-23 13:12:22.720] [jointLog] [info] parsing read library format
[2021-03-23 13:12:22.720] [jointLog] [info] There is 1 library.
[2021-03-23 13:12:22.800] [jointLog] [info] Loading pufferfish index
[2021-03-23 13:12:22.800] [jointLog] [info] Loading dense pufferfish index.
[2021-03-23 13:13:59.339] [jointLog] [info] done
[2021-03-23 13:13:59.339] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-23 13:14:47.358] [jointLog] [info] Number of decoys : 194
[2021-03-23 13:14:47.358] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-23 13:14:48.246] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-23 13:14:49.371] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-23 13:16:58.971] [jointLog] [info] Computed 407,960 rich equivalence classes for further processing
[2021-03-23 13:16:58.971] [jointLog] [info] Counted 14,339,925 total reads in the equivalence classes 
[2021-03-23 13:16:58.983] [jointLog] [info] Number of mappings discarded because of alignment score : 16,806,235
[2021-03-23 13:16:58.983] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 383,837
[2021-03-23 13:16:58.983] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 224,473
[2021-03-23 13:16:58.983] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-23 13:16:58.983] [jointLog] [info] Mapping rate = 94.4466%

[2021-03-23 13:16:58.983] [jointLog] [info] finished quantifyLibrary()
[2021-03-23 13:16:58.983] [jointLog] [info] Starting optimizer
[2021-03-23 13:16:58.972] [fileLog] [info] 
At end of round 0
==================
Observed 15183110 total fragments (15183110 in most recent round)

[2021-03-23 13:17:03.760] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-23 13:17:04.092] [jointLog] [info] iteration = 0 | max rel diff. = 223.01
[2021-03-23 13:17:07.467] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-23 13:19:05.816] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-23 13:19:05.817] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-23 13:19:16.456] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-23 13:19:27.319] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-23 13:19:38.513] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-23 13:19:49.733] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-23 13:20:00.796] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-23 13:20:11.523] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-23 13:20:22.448] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-23 13:20:33.498] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-23 13:20:44.277] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-23 13:20:55.021] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-23 13:20:55.021] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-23 13:21:30.341] [jointLog] [info] iteration = 100 | max rel diff. = 19.8912
[2021-03-23 13:22:07.846] [jointLog] [info] iteration = 200 | max rel diff. = 14.1891
[2021-03-23 13:22:44.852] [jointLog] [info] iteration = 300 | max rel diff. = 1.32547
[2021-03-23 13:23:21.608] [jointLog] [info] iteration = 400 | max rel diff. = 0.837584
[2021-03-23 13:23:57.918] [jointLog] [info] iteration = 500 | max rel diff. = 0.0606273
[2021-03-23 13:24:33.184] [jointLog] [info] iteration = 600 | max rel diff. = 0.19518
[2021-03-23 13:25:07.675] [jointLog] [info] iteration = 700 | max rel diff. = 2.60238
[2021-03-23 13:25:42.584] [jointLog] [info] iteration = 800 | max rel diff. = 0.0648469
[2021-03-23 13:26:16.977] [jointLog] [info] iteration = 900 | max rel diff. = 0.111225
[2021-03-23 13:26:52.617] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.101722
[2021-03-23 13:27:27.490] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0695224
[2021-03-23 13:28:02.254] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.19848
[2021-03-23 13:28:04.308] [jointLog] [info] iteration = 1,207 | max rel diff. = 0.00805634
[2021-03-23 13:28:06.517] [jointLog] [info] Finished optimizer
[2021-03-23 13:28:06.517] [jointLog] [info] writing output