[2021-08-11 19:12:18.709] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-11 19:12:18.709] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-11 19:12:18.709] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-11 19:12:18.709] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-11 19:12:18.709] [jointLog] [info] parsing read library format
[2021-08-11 19:12:18.709] [jointLog] [info] There is 1 library.
[2021-08-11 19:12:18.828] [jointLog] [info] Loading pufferfish index
[2021-08-11 19:12:18.828] [jointLog] [info] Loading dense pufferfish index.
[2021-08-11 19:14:00.340] [jointLog] [info] done
[2021-08-11 19:14:00.340] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-11 19:14:52.671] [jointLog] [info] Number of decoys : 194
[2021-08-11 19:14:52.671] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-11 19:14:54.182] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-11 19:14:55.030] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-11 19:15:33.411] [jointLog] [info] Thread saw mini-batch with a maximum of 5.04% zero probability fragments
[2021-08-11 19:15:33.416] [jointLog] [info] Thread saw mini-batch with a maximum of 4.88% zero probability fragments
[2021-08-11 19:15:33.451] [jointLog] [info] Thread saw mini-batch with a maximum of 4.70% zero probability fragments
[2021-08-11 19:15:33.474] [jointLog] [info] Thread saw mini-batch with a maximum of 5.16% zero probability fragments
[2021-08-11 19:15:33.495] [jointLog] [info] Thread saw mini-batch with a maximum of 4.96% zero probability fragments
[2021-08-11 19:15:33.583] [jointLog] [info] Thread saw mini-batch with a maximum of 4.76% zero probability fragments
[2021-08-11 19:15:33.602] [jointLog] [info] Thread saw mini-batch with a maximum of 4.88% zero probability fragments
[2021-08-11 19:15:33.648] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments
[2021-08-11 19:15:33.826] [jointLog] [info] Computed 164,071 rich equivalence classes for further processing
[2021-08-11 19:15:33.826] [jointLog] [info] Counted 5,308,852 total reads in the equivalence classes 
[2021-08-11 19:15:33.838] [jointLog] [info] Number of mappings discarded because of alignment score : 7,989,274
[2021-08-11 19:15:33.838] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 129,032
[2021-08-11 19:15:33.838] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 83,538
[2021-08-11 19:15:33.838] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-11 19:15:33.838] [jointLog] [info] Mapping rate = 91.5181%

[2021-08-11 19:15:33.838] [jointLog] [info] finished quantifyLibrary()
[2021-08-11 19:15:33.838] [jointLog] [info] Starting optimizer
[2021-08-11 19:15:33.827] [fileLog] [info] 
At end of round 0
==================
Observed 5800876 total fragments (5800876 in most recent round)

[2021-08-11 19:15:37.734] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-11 19:15:38.062] [jointLog] [info] iteration = 0 | max rel diff. = 95.5603
[2021-08-11 19:15:41.339] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-11 19:16:36.112] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-11 19:16:36.113] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-11 19:16:41.356] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-11 19:16:46.494] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-11 19:16:51.736] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-11 19:16:56.809] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-11 19:17:02.087] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-11 19:17:07.260] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-11 19:17:12.306] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-11 19:17:17.317] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-11 19:17:22.495] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-11 19:17:27.580] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-11 19:17:57.589] [jointLog] [info] iteration = 100 | max rel diff. = 18.3056
[2021-08-11 19:18:30.641] [jointLog] [info] iteration = 200 | max rel diff. = 20.0722
[2021-08-11 19:19:03.662] [jointLog] [info] iteration = 300 | max rel diff. = 4.33928
[2021-08-11 19:19:36.626] [jointLog] [info] iteration = 400 | max rel diff. = 7.77314
[2021-08-11 19:20:09.538] [jointLog] [info] iteration = 500 | max rel diff. = 0.53764
[2021-08-11 19:20:42.500] [jointLog] [info] iteration = 600 | max rel diff. = 0.370093
[2021-08-11 19:21:15.386] [jointLog] [info] iteration = 700 | max rel diff. = 0.188711
[2021-08-11 19:21:48.397] [jointLog] [info] iteration = 800 | max rel diff. = 0.0943683
[2021-08-11 19:22:20.133] [jointLog] [info] iteration = 900 | max rel diff. = 0.173103
[2021-08-11 19:22:52.160] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0543588
[2021-08-11 19:23:24.327] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.325552
[2021-08-11 19:23:56.603] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.044367
[2021-08-11 19:24:06.881] [jointLog] [info] iteration = 1,234 | max rel diff. = 0.00897033
[2021-08-11 19:24:08.919] [jointLog] [info] Finished optimizer
[2021-08-11 19:24:08.919] [jointLog] [info] writing output