[2023-08-30 19:06:41.138] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-30 19:06:41.138] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-30 19:06:41.138] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-30 19:06:41.138] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-30 19:06:41.138] [jointLog] [info] parsing read library format
[2023-08-30 19:06:41.138] [jointLog] [info] There is 1 library.
[2023-08-30 19:06:41.138] [jointLog] [info] Loading pufferfish index
[2023-08-30 19:06:41.138] [jointLog] [info] Loading dense pufferfish index.
[2023-08-30 19:08:45.265] [jointLog] [info] done
[2023-08-30 19:08:45.413] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-30 19:09:41.881] [jointLog] [info] Number of decoys : 194
[2023-08-30 19:09:41.881] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-30 19:09:46.241] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-30 19:24:12.497] [jointLog] [info] Thread saw mini-batch with a maximum of 13.60% zero probability fragments
[2023-08-30 19:24:12.549] [jointLog] [info] Thread saw mini-batch with a maximum of 13.18% zero probability fragments
[2023-08-30 19:24:12.598] [jointLog] [info] Thread saw mini-batch with a maximum of 13.48% zero probability fragments
[2023-08-30 19:24:12.913] [jointLog] [info] Thread saw mini-batch with a maximum of 13.22% zero probability fragments
[2023-08-30 19:24:12.963] [jointLog] [info] Thread saw mini-batch with a maximum of 13.48% zero probability fragments
[2023-08-30 19:24:12.990] [jointLog] [info] Thread saw mini-batch with a maximum of 13.40% zero probability fragments
[2023-08-30 19:24:13.006] [jointLog] [info] Thread saw mini-batch with a maximum of 13.56% zero probability fragments
[2023-08-30 19:24:13.150] [jointLog] [info] Thread saw mini-batch with a maximum of 13.24% zero probability fragments
[2023-08-30 19:24:13.661] [jointLog] [info] Computed 247,685 rich equivalence classes for further processing
[2023-08-30 19:24:13.661] [jointLog] [info] Counted 34,279,604 total reads in the equivalence classes 
[2023-08-30 19:24:13.684] [jointLog] [info] Number of mappings discarded because of alignment score : 14,882,319
[2023-08-30 19:24:13.684] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,074,140
[2023-08-30 19:24:13.684] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,033,884
[2023-08-30 19:24:13.684] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 551,872
[2023-08-30 19:24:13.684] [jointLog] [info] Mapping rate = 81.2811%

[2023-08-30 19:24:13.684] [jointLog] [info] finished quantifyLibrary()
[2023-08-30 19:24:13.684] [jointLog] [info] Starting optimizer
[2023-08-30 19:24:13.662] [fileLog] [info] 
At end of round 0
==================
Observed 42174144 total fragments (42174144 in most recent round)

[2023-08-30 19:24:19.246] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-30 19:24:19.667] [jointLog] [info] iteration = 0 | max rel diff. = 452.065
[2023-08-30 19:24:24.276] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-30 19:29:14.447] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-30 19:29:14.447] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-30 19:29:44.802] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-30 19:30:18.590] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-30 19:30:46.045] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-30 19:31:14.562] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-30 19:31:35.555] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-30 19:32:02.164] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-30 19:32:30.671] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-30 19:32:57.859] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-30 19:33:22.702] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-30 19:33:54.897] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-30 19:34:31.197] [jointLog] [info] iteration = 100 | max rel diff. = 15.6863
[2023-08-30 19:35:12.905] [jointLog] [info] iteration = 200 | max rel diff. = 4.91368
[2023-08-30 19:35:55.599] [jointLog] [info] iteration = 300 | max rel diff. = 2.8003
[2023-08-30 19:36:38.581] [jointLog] [info] iteration = 400 | max rel diff. = 0.128606
[2023-08-30 19:37:19.617] [jointLog] [info] iteration = 500 | max rel diff. = 0.287381
[2023-08-30 19:38:00.000] [jointLog] [info] iteration = 600 | max rel diff. = 1.22533
[2023-08-30 19:38:40.595] [jointLog] [info] iteration = 700 | max rel diff. = 0.054741
[2023-08-30 19:39:20.206] [jointLog] [info] iteration = 800 | max rel diff. = 1.27137
[2023-08-30 19:40:01.246] [jointLog] [info] iteration = 900 | max rel diff. = 0.259225
[2023-08-30 19:40:43.141] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0690865
[2023-08-30 19:40:50.202] [jointLog] [info] iteration = 1,017 | max rel diff. = 0.008075
[2023-08-30 19:40:52.688] [jointLog] [info] Finished optimizer
[2023-08-30 19:40:52.688] [jointLog] [info] writing output