[2023-09-05 16:16:43.218] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-05 16:16:43.218] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-05 16:16:43.218] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-05 16:16:43.218] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-05 16:16:43.218] [jointLog] [info] parsing read library format
[2023-09-05 16:16:43.218] [jointLog] [info] There is 1 library.
[2023-09-05 16:16:43.218] [jointLog] [info] Loading pufferfish index
[2023-09-05 16:16:43.218] [jointLog] [info] Loading dense pufferfish index.
[2023-09-05 16:17:59.758] [jointLog] [info] done
[2023-09-05 16:17:59.877] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-05 16:18:35.756] [jointLog] [info] Number of decoys : 194
[2023-09-05 16:18:35.756] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-05 16:18:37.769] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-05 16:21:46.244] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-05 16:21:46.293] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-05 16:21:46.301] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-05 16:21:46.339] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-05 16:21:46.405] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-05 16:21:46.414] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-05 16:21:46.415] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-05 16:21:46.516] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-05 16:21:47.060] [jointLog] [info] Computed 405,435 rich equivalence classes for further processing
[2023-09-05 16:21:47.060] [jointLog] [info] Counted 28,319,382 total reads in the equivalence classes 
[2023-09-05 16:21:47.067] [jointLog] [info] Number of mappings discarded because of alignment score : 4,862,809
[2023-09-05 16:21:47.067] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 577,837
[2023-09-05 16:21:47.067] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 431,440
[2023-09-05 16:21:47.067] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 180,009
[2023-09-05 16:21:47.067] [jointLog] [info] Mapping rate = 93.6236%

[2023-09-05 16:21:47.067] [jointLog] [info] finished quantifyLibrary()
[2023-09-05 16:21:47.068] [jointLog] [info] Starting optimizer
[2023-09-05 16:21:47.060] [fileLog] [info] 
At end of round 0
==================
Observed 30248116 total fragments (30248116 in most recent round)

[2023-09-05 16:21:52.556] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-05 16:21:52.973] [jointLog] [info] iteration = 0 | max rel diff. = 365.789
[2023-09-05 16:21:57.113] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-05 16:27:31.841] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-05 16:27:31.842] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-05 16:28:01.598] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-05 16:28:29.472] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-05 16:28:56.518] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-05 16:29:23.284] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-05 16:29:50.184] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-05 16:30:19.709] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-05 16:30:46.964] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-05 16:31:18.005] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-05 16:31:47.207] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-05 16:32:11.939] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-05 16:32:48.522] [jointLog] [info] iteration = 100 | max rel diff. = 18.0834
[2023-09-05 16:33:28.400] [jointLog] [info] iteration = 200 | max rel diff. = 17.1373
[2023-09-05 16:34:10.687] [jointLog] [info] iteration = 300 | max rel diff. = 8.79791
[2023-09-05 16:34:53.091] [jointLog] [info] iteration = 400 | max rel diff. = 2.9215
[2023-09-05 16:35:32.513] [jointLog] [info] iteration = 500 | max rel diff. = 1.35892
[2023-09-05 16:36:13.950] [jointLog] [info] iteration = 600 | max rel diff. = 0.166834
[2023-09-05 16:36:56.844] [jointLog] [info] iteration = 700 | max rel diff. = 0.330029
[2023-09-05 16:37:44.826] [jointLog] [info] iteration = 800 | max rel diff. = 0.0875453
[2023-09-05 16:38:31.081] [jointLog] [info] iteration = 900 | max rel diff. = 0.192383
[2023-09-05 16:39:11.956] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.118315
[2023-09-05 16:39:51.668] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.570033
[2023-09-05 16:40:31.581] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0650184
[2023-09-05 16:40:38.687] [jointLog] [info] iteration = 1,218 | max rel diff. = 0.00434913
[2023-09-05 16:40:40.803] [jointLog] [info] Finished optimizer
[2023-09-05 16:40:40.803] [jointLog] [info] writing output