[2021-08-11 17:11:01.106] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-11 17:11:01.106] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-11 17:11:01.106] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-11 17:11:01.106] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-11 17:11:01.106] [jointLog] [info] parsing read library format
[2021-08-11 17:11:01.106] [jointLog] [info] There is 1 library.
[2021-08-11 17:11:01.238] [jointLog] [info] Loading pufferfish index
[2021-08-11 17:11:01.238] [jointLog] [info] Loading dense pufferfish index.
[2021-08-11 17:12:42.351] [jointLog] [info] done
[2021-08-11 17:12:42.351] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-11 17:13:33.142] [jointLog] [info] Number of decoys : 194
[2021-08-11 17:13:33.142] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-11 17:13:34.063] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-11 17:13:34.630] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-11 17:14:15.147] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2021-08-11 17:14:15.159] [jointLog] [info] Thread saw mini-batch with a maximum of 5.22% zero probability fragments
[2021-08-11 17:14:15.172] [jointLog] [info] Thread saw mini-batch with a maximum of 4.84% zero probability fragments
[2021-08-11 17:14:15.224] [jointLog] [info] Thread saw mini-batch with a maximum of 4.94% zero probability fragments
[2021-08-11 17:14:15.240] [jointLog] [info] Thread saw mini-batch with a maximum of 4.88% zero probability fragments
[2021-08-11 17:14:15.276] [jointLog] [info] Thread saw mini-batch with a maximum of 5.04% zero probability fragments
[2021-08-11 17:14:15.331] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2021-08-11 17:14:15.368] [jointLog] [info] Thread saw mini-batch with a maximum of 4.70% zero probability fragments
[2021-08-11 17:14:15.534] [jointLog] [info] Computed 173,375 rich equivalence classes for further processing
[2021-08-11 17:14:15.534] [jointLog] [info] Counted 6,175,436 total reads in the equivalence classes 
[2021-08-11 17:14:15.544] [jointLog] [info] Number of mappings discarded because of alignment score : 9,003,179
[2021-08-11 17:14:15.544] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 156,987
[2021-08-11 17:14:15.544] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 101,369
[2021-08-11 17:14:15.544] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-11 17:14:15.544] [jointLog] [info] Mapping rate = 91.3193%

[2021-08-11 17:14:15.544] [jointLog] [info] finished quantifyLibrary()
[2021-08-11 17:14:15.545] [jointLog] [info] Starting optimizer
[2021-08-11 17:14:15.535] [fileLog] [info] 
At end of round 0
==================
Observed 6762466 total fragments (6762466 in most recent round)

[2021-08-11 17:14:18.767] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-11 17:14:19.097] [jointLog] [info] iteration = 0 | max rel diff. = 110.236
[2021-08-11 17:14:22.417] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-11 17:15:18.289] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-11 17:15:18.290] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-11 17:15:23.599] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-11 17:15:28.976] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-11 17:15:34.303] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-11 17:15:39.831] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-11 17:15:45.196] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-11 17:15:50.453] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-11 17:15:55.594] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-11 17:16:00.932] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-11 17:16:06.157] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-11 17:16:11.423] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-11 17:16:11.456] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-11 17:16:39.481] [jointLog] [info] iteration = 100 | max rel diff. = 11.9255
[2021-08-11 17:17:10.667] [jointLog] [info] iteration = 200 | max rel diff. = 7.64902
[2021-08-11 17:17:41.991] [jointLog] [info] iteration = 300 | max rel diff. = 0.754908
[2021-08-11 17:18:13.601] [jointLog] [info] iteration = 400 | max rel diff. = 10.4949
[2021-08-11 17:18:45.036] [jointLog] [info] iteration = 500 | max rel diff. = 2.03031
[2021-08-11 17:19:16.259] [jointLog] [info] iteration = 600 | max rel diff. = 0.0837224
[2021-08-11 17:19:47.378] [jointLog] [info] iteration = 700 | max rel diff. = 0.0625451
[2021-08-11 17:20:18.616] [jointLog] [info] iteration = 800 | max rel diff. = 1.35033
[2021-08-11 17:20:50.556] [jointLog] [info] iteration = 900 | max rel diff. = 0.651489
[2021-08-11 17:21:21.763] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.109707
[2021-08-11 17:21:50.106] [jointLog] [info] iteration = 1,092 | max rel diff. = 0.00448168
[2021-08-11 17:21:51.689] [jointLog] [info] Finished optimizer
[2021-08-11 17:21:51.689] [jointLog] [info] writing output