[2023-08-29 16:10:42.815] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-29 16:10:42.815] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-29 16:10:42.815] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-29 16:10:42.816] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-29 16:10:42.816] [jointLog] [info] parsing read library format
[2023-08-29 16:10:42.816] [jointLog] [info] There is 1 library.
[2023-08-29 16:10:42.816] [jointLog] [info] Loading pufferfish index
[2023-08-29 16:10:42.816] [jointLog] [info] Loading dense pufferfish index.
[2023-08-29 16:11:59.882] [jointLog] [info] done
[2023-08-29 16:12:00.011] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-29 16:12:38.314] [jointLog] [info] Number of decoys : 194
[2023-08-29 16:12:38.314] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-29 16:12:40.430] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-29 16:12:41.547] [jointLog] [info] Automatically detected most likely library type as SR

[2023-08-29 16:14:49.311] [jointLog] [info] Thread saw mini-batch with a maximum of 1.98% zero probability fragments
[2023-08-29 16:14:49.312] [jointLog] [info] Thread saw mini-batch with a maximum of 1.98% zero probability fragments
[2023-08-29 16:14:49.376] [jointLog] [info] Thread saw mini-batch with a maximum of 2.08% zero probability fragments
[2023-08-29 16:14:49.389] [jointLog] [info] Thread saw mini-batch with a maximum of 1.92% zero probability fragments
[2023-08-29 16:14:49.405] [jointLog] [info] Thread saw mini-batch with a maximum of 1.90% zero probability fragments
[2023-08-29 16:14:49.425] [jointLog] [info] Thread saw mini-batch with a maximum of 2.14% zero probability fragments
[2023-08-29 16:14:49.434] [jointLog] [info] Thread saw mini-batch with a maximum of 2.06% zero probability fragments
[2023-08-29 16:14:49.494] [jointLog] [info] Thread saw mini-batch with a maximum of 2.02% zero probability fragments
[2023-08-29 16:14:49.812] [fileLog] [info] 
At end of round 0
==================
Observed 19767521 total fragments (19767521 in most recent round)

[2023-08-29 16:14:49.811] [jointLog] [info] Computed 224,698 rich equivalence classes for further processing
[2023-08-29 16:14:49.811] [jointLog] [info] Counted 18,661,669 total reads in the equivalence classes 
[2023-08-29 16:14:49.823] [jointLog] [info] Number of mappings discarded because of alignment score : 20,707,861
[2023-08-29 16:14:49.823] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 289,523
[2023-08-29 16:14:49.823] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 156,245
[2023-08-29 16:14:49.823] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-29 16:14:49.823] [jointLog] [info] Mapping rate = 94.4057%

[2023-08-29 16:14:49.823] [jointLog] [info] finished quantifyLibrary()
[2023-08-29 16:14:49.823] [jointLog] [info] Starting optimizer
[2023-08-29 16:14:55.275] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-29 16:14:55.611] [jointLog] [info] iteration = 0 | max rel diff. = 337.388
[2023-08-29 16:14:58.976] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-29 16:16:19.965] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-29 16:16:19.966] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-29 16:16:27.252] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-29 16:16:34.526] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-29 16:16:41.972] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-29 16:16:49.418] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-29 16:16:56.568] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-29 16:17:04.240] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-29 16:17:11.801] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-29 16:17:19.007] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-29 16:17:26.181] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-29 16:17:33.480] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-29 16:17:33.513] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-29 16:18:02.996] [jointLog] [info] iteration = 100 | max rel diff. = 13.8147
[2023-08-29 16:18:35.520] [jointLog] [info] iteration = 200 | max rel diff. = 9.69426
[2023-08-29 16:19:08.051] [jointLog] [info] iteration = 300 | max rel diff. = 12.7378
[2023-08-29 16:19:41.406] [jointLog] [info] iteration = 400 | max rel diff. = 0.541363
[2023-08-29 16:20:13.995] [jointLog] [info] iteration = 500 | max rel diff. = 1.63863
[2023-08-29 16:20:47.259] [jointLog] [info] iteration = 600 | max rel diff. = 0.171571
[2023-08-29 16:21:20.650] [jointLog] [info] iteration = 700 | max rel diff. = 0.140864
[2023-08-29 16:21:53.767] [jointLog] [info] iteration = 800 | max rel diff. = 0.215985
[2023-08-29 16:22:27.111] [jointLog] [info] iteration = 900 | max rel diff. = 0.0903606
[2023-08-29 16:23:00.250] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.154087
[2023-08-29 16:23:33.592] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0839143
[2023-08-29 16:24:06.671] [jointLog] [info] iteration = 1,200 | max rel diff. = 9.25248
[2023-08-29 16:24:39.056] [jointLog] [info] iteration = 1,297 | max rel diff. = 0.00525189
[2023-08-29 16:24:41.043] [jointLog] [info] Finished optimizer
[2023-08-29 16:24:41.043] [jointLog] [info] writing output