[2021-08-13 19:12:55.618] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-13 19:12:55.618] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-13 19:12:55.618] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-13 19:12:55.618] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-13 19:12:55.618] [jointLog] [info] parsing read library format
[2021-08-13 19:12:55.618] [jointLog] [info] There is 1 library.
[2021-08-13 19:12:55.691] [jointLog] [info] Loading pufferfish index
[2021-08-13 19:12:55.691] [jointLog] [info] Loading dense pufferfish index.
[2021-08-13 19:14:42.047] [jointLog] [info] done
[2021-08-13 19:14:42.047] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-13 19:15:31.291] [jointLog] [info] Number of decoys : 194
[2021-08-13 19:15:31.291] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-13 19:15:32.643] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-13 19:15:33.663] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2021-08-13 19:16:13.071] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2021-08-13 19:16:13.261] [jointLog] [info] Computed 152,168 rich equivalence classes for further processing
[2021-08-13 19:16:13.261] [jointLog] [info] Counted 5,148,423 total reads in the equivalence classes 
[2021-08-13 19:16:13.275] [jointLog] [info] Number of mappings discarded because of alignment score : 7,341,287
[2021-08-13 19:16:13.275] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 117,661
[2021-08-13 19:16:13.275] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 68,609
[2021-08-13 19:16:13.275] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-13 19:16:13.275] [jointLog] [info] Mapping rate = 92.7213%

[2021-08-13 19:16:13.275] [jointLog] [info] finished quantifyLibrary()
[2021-08-13 19:16:13.275] [jointLog] [info] Starting optimizer
[2021-08-13 19:16:13.262] [fileLog] [info] 
At end of round 0
==================
Observed 5552579 total fragments (5552579 in most recent round)

[2021-08-13 19:16:27.666] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-13 19:16:28.009] [jointLog] [info] iteration = 0 | max rel diff. = 101.059
[2021-08-13 19:16:31.454] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-13 19:17:30.127] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-13 19:17:30.127] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-13 19:17:35.512] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-13 19:17:40.965] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-13 19:17:46.363] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-13 19:17:51.606] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-13 19:17:56.932] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-13 19:18:02.382] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-13 19:18:07.824] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-13 19:18:13.071] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-13 19:18:18.533] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-13 19:18:23.851] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-13 19:18:56.359] [jointLog] [info] iteration = 100 | max rel diff. = 10.9125
[2021-08-13 19:19:31.680] [jointLog] [info] iteration = 200 | max rel diff. = 15.4941
[2021-08-13 19:20:06.500] [jointLog] [info] iteration = 300 | max rel diff. = 12.2191
[2021-08-13 19:20:41.111] [jointLog] [info] iteration = 400 | max rel diff. = 6.69054
[2021-08-13 19:21:13.507] [jointLog] [info] iteration = 500 | max rel diff. = 0.183938
[2021-08-13 19:21:45.885] [jointLog] [info] iteration = 600 | max rel diff. = 0.433235
[2021-08-13 19:22:18.025] [jointLog] [info] iteration = 700 | max rel diff. = 0.394546
[2021-08-13 19:22:50.322] [jointLog] [info] iteration = 800 | max rel diff. = 0.0892099
[2021-08-13 19:23:22.333] [jointLog] [info] iteration = 900 | max rel diff. = 0.21184
[2021-08-13 19:23:54.199] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.161622
[2021-08-13 19:24:26.060] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0876182
[2021-08-13 19:24:36.150] [jointLog] [info] iteration = 1,132 | max rel diff. = 0.0064739
[2021-08-13 19:24:38.095] [jointLog] [info] Finished optimizer
[2021-08-13 19:24:38.095] [jointLog] [info] writing output