[2023-09-11 17:38:11.636] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-11 17:38:11.637] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-11 17:38:11.637] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-11 17:38:11.637] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-11 17:38:11.637] [jointLog] [info] parsing read library format
[2023-09-11 17:38:11.637] [jointLog] [info] There is 1 library.
[2023-09-11 17:38:11.637] [jointLog] [info] Loading pufferfish index
[2023-09-11 17:38:11.637] [jointLog] [info] Loading dense pufferfish index.
[2023-09-11 17:39:38.794] [jointLog] [info] done
[2023-09-11 17:39:38.993] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-11 17:40:20.930] [jointLog] [info] Number of decoys : 194
[2023-09-11 17:40:20.930] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-11 17:40:26.517] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-11 17:56:12.684] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments
[2023-09-11 17:56:12.706] [jointLog] [info] Thread saw mini-batch with a maximum of 2.20% zero probability fragments
[2023-09-11 17:56:13.096] [jointLog] [info] Thread saw mini-batch with a maximum of 2.18% zero probability fragments
[2023-09-11 17:56:13.330] [jointLog] [info] Thread saw mini-batch with a maximum of 2.10% zero probability fragments
[2023-09-11 17:56:13.358] [jointLog] [info] Thread saw mini-batch with a maximum of 2.08% zero probability fragments
[2023-09-11 17:56:13.387] [jointLog] [info] Thread saw mini-batch with a maximum of 2.30% zero probability fragments
[2023-09-11 17:56:13.390] [jointLog] [info] Thread saw mini-batch with a maximum of 2.10% zero probability fragments
[2023-09-11 17:56:13.513] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments
[2023-09-11 17:56:13.983] [fileLog] [info] 
At end of round 0
==================
Observed 37004712 total fragments (37004712 in most recent round)

[2023-09-11 17:56:13.982] [jointLog] [info] Computed 253,272 rich equivalence classes for further processing
[2023-09-11 17:56:13.982] [jointLog] [info] Counted 22,269,272 total reads in the equivalence classes 
[2023-09-11 17:56:13.992] [jointLog] [info] Number of mappings discarded because of alignment score : 99,127,448
[2023-09-11 17:56:13.992] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 13,926,463
[2023-09-11 17:56:13.992] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 510,197
[2023-09-11 17:56:13.992] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 8,358,843
[2023-09-11 17:56:13.992] [jointLog] [info] Mapping rate = 60.1796%

[2023-09-11 17:56:13.992] [jointLog] [info] finished quantifyLibrary()
[2023-09-11 17:56:13.992] [jointLog] [info] Starting optimizer
[2023-09-11 17:56:22.633] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-11 17:56:22.974] [jointLog] [info] iteration = 0 | max rel diff. = 244.81
[2023-09-11 17:56:26.371] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-11 18:01:01.388] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-11 18:01:01.388] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-11 18:01:23.375] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-11 18:01:45.216] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-11 18:02:07.277] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-11 18:02:30.046] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-11 18:02:51.877] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-11 18:03:14.602] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-11 18:03:37.239] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-11 18:03:58.758] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-11 18:04:20.883] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-11 18:04:42.048] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-11 18:05:12.324] [jointLog] [info] iteration = 100 | max rel diff. = 12.421
[2023-09-11 18:05:45.606] [jointLog] [info] iteration = 200 | max rel diff. = 15.7335
[2023-09-11 18:06:18.867] [jointLog] [info] iteration = 300 | max rel diff. = 0.450095
[2023-09-11 18:06:51.455] [jointLog] [info] iteration = 400 | max rel diff. = 0.105794
[2023-09-11 18:07:24.766] [jointLog] [info] iteration = 500 | max rel diff. = 0.887892
[2023-09-11 18:07:59.075] [jointLog] [info] iteration = 600 | max rel diff. = 0.447756
[2023-09-11 18:08:32.770] [jointLog] [info] iteration = 700 | max rel diff. = 0.372202
[2023-09-11 18:09:05.959] [jointLog] [info] iteration = 800 | max rel diff. = 0.391457
[2023-09-11 18:09:39.322] [jointLog] [info] iteration = 900 | max rel diff. = 0.190491
[2023-09-11 18:10:07.422] [jointLog] [info] iteration = 984 | max rel diff. = 0.00869478
[2023-09-11 18:10:09.861] [jointLog] [info] Finished optimizer
[2023-09-11 18:10:09.861] [jointLog] [info] writing output