[2022-12-20 23:41:46.076] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:41:46.076] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:41:46.076] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:41:46.076] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:41:46.076] [jointLog] [info] parsing read library format
[2022-12-20 23:41:46.076] [jointLog] [info] There is 1 library.
[2022-12-20 23:41:46.076] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:41:46.077] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:42:06.625] [jointLog] [info] done
[2022-12-20 23:42:06.676] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:42:06.990] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:42:06.990] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:42:08.259] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:46:20.607] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:46:20.611] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:46:20.635] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:46:20.754] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:46:20.794] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:46:20.870] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:46:20.912] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:46:20.924] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:46:21.089] [jointLog] [info] Computed 254,949 rich equivalence classes for further processing
[2022-12-20 23:46:21.089] [jointLog] [info] Counted 12,386,493 total reads in the equivalence classes 
[2022-12-20 23:46:21.093] [jointLog] [info] Number of mappings discarded because of alignment score : 45,429,072
[2022-12-20 23:46:21.093] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,519,782
[2022-12-20 23:46:21.093] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 272,055
[2022-12-20 23:46:21.093] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,211,872
[2022-12-20 23:46:21.093] [jointLog] [info] Mapping rate = 68.564%

[2022-12-20 23:46:21.093] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:46:21.093] [jointLog] [info] Starting optimizer
[2022-12-20 23:46:21.163] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:46:21.179] [jointLog] [info] iteration = 0 | max rel diff. = 6292.14
[2022-12-20 23:46:21.089] [fileLog] [info] 
At end of round 0
==================
Observed 18065581 total fragments (18065581 in most recent round)

[2022-12-20 23:46:21.309] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:46:22.102] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:46:22.102] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-12-20 23:46:22.547] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:46:22.989] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:46:23.447] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-20 23:46:23.950] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:46:24.428] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:46:24.932] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:46:25.411] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:46:25.869] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-20 23:46:26.357] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:46:26.773] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:46:26.774] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:46:27.839] [jointLog] [info] iteration = 100 | max rel diff. = 17.0611
[2022-12-20 23:46:29.032] [jointLog] [info] iteration = 200 | max rel diff. = 1.15947
[2022-12-20 23:46:30.240] [jointLog] [info] iteration = 300 | max rel diff. = 5.4583
[2022-12-20 23:46:31.787] [jointLog] [info] iteration = 400 | max rel diff. = 0.138791
[2022-12-20 23:46:33.062] [jointLog] [info] iteration = 500 | max rel diff. = 0.101955
[2022-12-20 23:46:34.250] [jointLog] [info] iteration = 600 | max rel diff. = 0.227347
[2022-12-20 23:46:35.454] [jointLog] [info] iteration = 700 | max rel diff. = 0.137016
[2022-12-20 23:46:36.636] [jointLog] [info] iteration = 800 | max rel diff. = 0.0172852
[2022-12-20 23:46:37.793] [jointLog] [info] iteration = 900 | max rel diff. = 0.075583
[2022-12-20 23:46:39.063] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0956514
[2022-12-20 23:46:40.432] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0209316
[2022-12-20 23:46:41.766] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0340477
[2022-12-20 23:46:43.093] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.98726
[2022-12-20 23:46:44.177] [jointLog] [info] iteration = 1,380 | max rel diff. = 0.00985591
[2022-12-20 23:46:44.197] [jointLog] [info] Finished optimizer
[2022-12-20 23:46:44.197] [jointLog] [info] writing output