[2023-08-25 13:33:00.985] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 13:33:00.985] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 13:33:00.985] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 13:33:00.985] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 13:33:00.985] [jointLog] [info] parsing read library format
[2023-08-25 13:33:00.985] [jointLog] [info] There is 1 library.
[2023-08-25 13:33:00.986] [jointLog] [info] Loading pufferfish index
[2023-08-25 13:33:00.986] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 13:34:15.303] [jointLog] [info] done
[2023-08-25 13:34:15.423] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 13:34:53.530] [jointLog] [info] Number of decoys : 194
[2023-08-25 13:34:53.530] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 13:34:57.917] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-25 13:42:30.962] [jointLog] [info] Thread saw mini-batch with a maximum of 9.70% zero probability fragments
[2023-08-25 13:42:31.027] [jointLog] [info] Thread saw mini-batch with a maximum of 9.86% zero probability fragments
[2023-08-25 13:42:31.097] [jointLog] [info] Thread saw mini-batch with a maximum of 9.58% zero probability fragments
[2023-08-25 13:42:31.128] [jointLog] [info] Thread saw mini-batch with a maximum of 9.54% zero probability fragments
[2023-08-25 13:42:31.252] [jointLog] [info] Thread saw mini-batch with a maximum of 9.56% zero probability fragments
[2023-08-25 13:42:31.404] [jointLog] [info] Thread saw mini-batch with a maximum of 9.66% zero probability fragments
[2023-08-25 13:42:31.412] [jointLog] [info] Thread saw mini-batch with a maximum of 9.94% zero probability fragments
[2023-08-25 13:42:31.450] [jointLog] [info] Thread saw mini-batch with a maximum of 9.64% zero probability fragments
[2023-08-25 13:42:32.026] [jointLog] [info] Computed 420,498 rich equivalence classes for further processing
[2023-08-25 13:42:32.026] [jointLog] [info] Counted 23,454,020 total reads in the equivalence classes 
[2023-08-25 13:42:32.036] [jointLog] [info] Number of mappings discarded because of alignment score : 22,087,656
[2023-08-25 13:42:32.036] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,359,594
[2023-08-25 13:42:32.036] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,014,485
[2023-08-25 13:42:32.036] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,390,827
[2023-08-25 13:42:32.036] [jointLog] [info] Mapping rate = 79.9267%

[2023-08-25 13:42:32.036] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 13:42:32.037] [jointLog] [info] Starting optimizer
[2023-08-25 13:42:32.027] [fileLog] [info] 
At end of round 0
==================
Observed 29344397 total fragments (29344397 in most recent round)

[2023-08-25 13:42:37.543] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 13:42:37.896] [jointLog] [info] iteration = 0 | max rel diff. = 304.884
[2023-08-25 13:42:41.393] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 13:47:59.881] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 13:47:59.881] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 13:48:25.990] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 13:48:52.749] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 13:49:19.324] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 13:49:46.673] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 13:50:12.888] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 13:50:39.559] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 13:51:05.399] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 13:51:30.537] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 13:51:56.843] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 13:52:22.914] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 13:52:54.349] [jointLog] [info] iteration = 100 | max rel diff. = 20.1907
[2023-08-25 13:53:28.135] [jointLog] [info] iteration = 200 | max rel diff. = 2.48798
[2023-08-25 13:54:01.845] [jointLog] [info] iteration = 300 | max rel diff. = 1.13984
[2023-08-25 13:54:35.100] [jointLog] [info] iteration = 400 | max rel diff. = 1.42676
[2023-08-25 13:55:08.415] [jointLog] [info] iteration = 500 | max rel diff. = 0.238425
[2023-08-25 13:55:42.142] [jointLog] [info] iteration = 600 | max rel diff. = 0.0986222
[2023-08-25 13:56:16.121] [jointLog] [info] iteration = 700 | max rel diff. = 0.380112
[2023-08-25 13:56:50.015] [jointLog] [info] iteration = 800 | max rel diff. = 4.29922
[2023-08-25 13:57:24.003] [jointLog] [info] iteration = 900 | max rel diff. = 0.0999127
[2023-08-25 13:57:58.494] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.179416
[2023-08-25 13:58:32.676] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.133904
[2023-08-25 13:58:48.270] [jointLog] [info] iteration = 1,146 | max rel diff. = 0.00830257
[2023-08-25 13:58:50.110] [jointLog] [info] Finished optimizer
[2023-08-25 13:58:50.110] [jointLog] [info] writing output