[2023-08-30 18:19:54.909] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-30 18:19:54.909] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-30 18:19:54.909] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-30 18:19:54.909] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-30 18:19:54.909] [jointLog] [info] parsing read library format
[2023-08-30 18:19:54.909] [jointLog] [info] There is 1 library.
[2023-08-30 18:19:54.909] [jointLog] [info] Loading pufferfish index
[2023-08-30 18:19:54.910] [jointLog] [info] Loading dense pufferfish index.
[2023-08-30 18:21:58.867] [jointLog] [info] done
[2023-08-30 18:21:59.035] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-30 18:22:53.374] [jointLog] [info] Number of decoys : 194
[2023-08-30 18:22:53.374] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-30 18:22:57.395] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-30 18:37:59.484] [jointLog] [info] Thread saw mini-batch with a maximum of 12.94% zero probability fragments
[2023-08-30 18:37:59.516] [jointLog] [info] Thread saw mini-batch with a maximum of 13.08% zero probability fragments
[2023-08-30 18:37:59.535] [jointLog] [info] Thread saw mini-batch with a maximum of 13.08% zero probability fragments
[2023-08-30 18:37:59.634] [jointLog] [info] Thread saw mini-batch with a maximum of 13.32% zero probability fragments
[2023-08-30 18:37:59.725] [jointLog] [info] Thread saw mini-batch with a maximum of 13.24% zero probability fragments
[2023-08-30 18:37:59.759] [jointLog] [info] Thread saw mini-batch with a maximum of 13.18% zero probability fragments
[2023-08-30 18:37:59.812] [jointLog] [info] Thread saw mini-batch with a maximum of 13.38% zero probability fragments
[2023-08-30 18:38:00.096] [jointLog] [info] Thread saw mini-batch with a maximum of 13.32% zero probability fragments
[2023-08-30 18:38:00.758] [jointLog] [info] Computed 286,835 rich equivalence classes for further processing
[2023-08-30 18:38:00.758] [jointLog] [info] Counted 35,097,821 total reads in the equivalence classes 
[2023-08-30 18:38:00.777] [jointLog] [info] Number of mappings discarded because of alignment score : 13,008,417
[2023-08-30 18:38:00.777] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,519,830
[2023-08-30 18:38:00.777] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,404,979
[2023-08-30 18:38:00.777] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 717,676
[2023-08-30 18:38:00.777] [jointLog] [info] Mapping rate = 81.3375%

[2023-08-30 18:38:00.777] [jointLog] [info] finished quantifyLibrary()
[2023-08-30 18:38:00.777] [jointLog] [info] Starting optimizer
[2023-08-30 18:38:00.759] [fileLog] [info] 
At end of round 0
==================
Observed 43150862 total fragments (43150862 in most recent round)

[2023-08-30 18:38:07.768] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-30 18:38:08.216] [jointLog] [info] iteration = 0 | max rel diff. = 317.59
[2023-08-30 18:38:13.136] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-30 18:44:59.407] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-30 18:44:59.408] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-30 18:45:40.287] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-30 18:46:18.989] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-30 18:46:58.197] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-30 18:47:39.385] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-30 18:48:19.775] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-30 18:48:58.550] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-30 18:49:38.390] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-30 18:50:17.123] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-30 18:50:57.173] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-30 18:51:38.766] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 18:52:21.791] [jointLog] [info] iteration = 100 | max rel diff. = 4.11221
[2023-08-30 18:53:14.277] [jointLog] [info] iteration = 200 | max rel diff. = 1.39952
[2023-08-30 18:54:04.488] [jointLog] [info] iteration = 300 | max rel diff. = 0.741164
[2023-08-30 18:54:53.820] [jointLog] [info] iteration = 400 | max rel diff. = 0.130562
[2023-08-30 18:55:43.807] [jointLog] [info] iteration = 500 | max rel diff. = 0.373604
[2023-08-30 18:56:34.994] [jointLog] [info] iteration = 600 | max rel diff. = 0.128558
[2023-08-30 18:57:26.076] [jointLog] [info] iteration = 700 | max rel diff. = 0.0761885
[2023-08-30 18:58:16.165] [jointLog] [info] iteration = 800 | max rel diff. = 0.744635
[2023-08-30 18:59:05.057] [jointLog] [info] iteration = 900 | max rel diff. = 0.560494
[2023-08-30 18:59:54.746] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0404582
[2023-08-30 19:00:42.695] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0671107
[2023-08-30 19:01:05.960] [jointLog] [info] iteration = 1,151 | max rel diff. = 0.00917236
[2023-08-30 19:01:08.516] [jointLog] [info] Finished optimizer
[2023-08-30 19:01:08.516] [jointLog] [info] writing output