[2021-11-18 16:19:52.077] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-11-18 16:19:52.077] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-11-18 16:19:52.077] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-11-18 16:19:52.077] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-11-18 16:19:52.077] [jointLog] [info] parsing read library format
[2021-11-18 16:19:52.077] [jointLog] [info] There is 1 library.
[2021-11-18 16:19:52.192] [jointLog] [info] Loading pufferfish index
[2021-11-18 16:19:52.192] [jointLog] [info] Loading dense pufferfish index.
[2021-11-18 16:21:36.644] [jointLog] [info] done
[2021-11-18 16:21:36.644] [jointLog] [info] Index contained 5,382,683 targets
[2021-11-18 16:22:30.716] [jointLog] [info] Number of decoys : 194
[2021-11-18 16:22:30.716] [jointLog] [info] First decoy index : 5,185,409 
[2021-11-18 16:22:33.139] [jointLog] [info] Automatically detected most likely library type as ISR
[2021-11-18 16:25:26.151] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2021-11-18 16:25:26.179] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2021-11-18 16:25:26.229] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2021-11-18 16:25:26.314] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2021-11-18 16:25:26.407] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2021-11-18 16:25:26.429] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2021-11-18 16:25:26.442] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2021-11-18 16:25:26.467] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2021-11-18 16:25:26.819] [jointLog] [info] Computed 290,436 rich equivalence classes for further processing
[2021-11-18 16:25:26.819] [jointLog] [info] Counted 18,233,319 total reads in the equivalence classes 
[2021-11-18 16:25:26.829] [jointLog] [info] Number of mappings discarded because of alignment score : 16,743,135
[2021-11-18 16:25:26.829] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 902,701
[2021-11-18 16:25:26.829] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 400,529
[2021-11-18 16:25:26.829] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 178,487
[2021-11-18 16:25:26.829] [jointLog] [info] Mapping rate = 92.2927%

[2021-11-18 16:25:26.829] [jointLog] [info] finished quantifyLibrary()
[2021-11-18 16:25:26.829] [jointLog] [info] Starting optimizer
[2021-11-18 16:25:26.820] [fileLog] [info] 
At end of round 0
==================
Observed 19755963 total fragments (19755963 in most recent round)

[2021-11-18 16:26:05.571] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-11-18 16:26:05.923] [jointLog] [info] iteration = 0 | max rel diff. = 264.873
[2021-11-18 16:26:09.433] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-11-18 16:31:11.467] [jointLog] [info] Computed expected counts (for bias correction)
[2021-11-18 16:31:11.467] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-11-18 16:31:34.738] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-11-18 16:31:59.113] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-11-18 16:32:23.759] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-11-18 16:32:48.440] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-11-18 16:33:12.665] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-11-18 16:33:37.169] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-11-18 16:34:00.376] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-11-18 16:34:24.385] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-11-18 16:34:47.737] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-11-18 16:35:11.669] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-11-18 16:35:40.778] [jointLog] [info] iteration = 100 | max rel diff. = 10.6433
[2021-11-18 16:36:12.460] [jointLog] [info] iteration = 200 | max rel diff. = 3.82108
[2021-11-18 16:36:44.209] [jointLog] [info] iteration = 300 | max rel diff. = 8.42132
[2021-11-18 16:37:16.109] [jointLog] [info] iteration = 400 | max rel diff. = 1.55286
[2021-11-18 16:37:48.974] [jointLog] [info] iteration = 500 | max rel diff. = 0.170276
[2021-11-18 16:38:22.969] [jointLog] [info] iteration = 600 | max rel diff. = 2.99406
[2021-11-18 16:38:56.809] [jointLog] [info] iteration = 700 | max rel diff. = 0.122337
[2021-11-18 16:39:30.091] [jointLog] [info] iteration = 800 | max rel diff. = 0.157006
[2021-11-18 16:40:02.703] [jointLog] [info] iteration = 900 | max rel diff. = 0.224534
[2021-11-18 16:40:35.535] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.206227
[2021-11-18 16:41:08.101] [jointLog] [info] iteration = 1,100 | max rel diff. = 9.46746
[2021-11-18 16:41:27.003] [jointLog] [info] iteration = 1,159 | max rel diff. = 0.00800783
[2021-11-18 16:41:29.191] [jointLog] [info] Finished optimizer
[2021-11-18 16:41:29.191] [jointLog] [info] writing output