[2023-09-09 17:31:33.452] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-09 17:31:33.452] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-09 17:31:33.452] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-09 17:31:33.452] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-09 17:31:33.452] [jointLog] [info] parsing read library format
[2023-09-09 17:31:33.452] [jointLog] [info] There is 1 library.
[2023-09-09 17:31:33.452] [jointLog] [info] Loading pufferfish index
[2023-09-09 17:31:33.452] [jointLog] [info] Loading dense pufferfish index.
[2023-09-09 17:32:52.338] [jointLog] [info] done
[2023-09-09 17:32:52.505] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-09 17:33:28.961] [jointLog] [info] Number of decoys : 194
[2023-09-09 17:33:28.961] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-09 17:33:31.371] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-09 17:40:14.564] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-09-09 17:40:14.598] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-09-09 17:40:14.609] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2023-09-09 17:40:14.617] [jointLog] [info] Thread saw mini-batch with a maximum of 4.72% zero probability fragments
[2023-09-09 17:40:14.645] [jointLog] [info] Thread saw mini-batch with a maximum of 4.88% zero probability fragments
[2023-09-09 17:40:14.662] [jointLog] [info] Thread saw mini-batch with a maximum of 4.96% zero probability fragments
[2023-09-09 17:40:14.671] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-09-09 17:40:14.841] [jointLog] [info] Thread saw mini-batch with a maximum of 4.68% zero probability fragments
[2023-09-09 17:40:15.814] [jointLog] [info] Computed 841,557 rich equivalence classes for further processing
[2023-09-09 17:40:15.814] [jointLog] [info] Counted 37,502,626 total reads in the equivalence classes 
[2023-09-09 17:40:15.822] [jointLog] [info] Number of mappings discarded because of alignment score : 8,587,998
[2023-09-09 17:40:15.822] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,809,784
[2023-09-09 17:40:15.822] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,378,289
[2023-09-09 17:40:15.822] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 448,043
[2023-09-09 17:40:15.822] [jointLog] [info] Mapping rate = 90.5502%

[2023-09-09 17:40:15.822] [jointLog] [info] finished quantifyLibrary()
[2023-09-09 17:40:15.822] [jointLog] [info] Starting optimizer
[2023-09-09 17:40:15.815] [fileLog] [info] 
At end of round 0
==================
Observed 41416390 total fragments (41416390 in most recent round)

[2023-09-09 17:40:20.300] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-09 17:40:20.655] [jointLog] [info] iteration = 0 | max rel diff. = 266.991
[2023-09-09 17:40:24.260] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-09 17:45:17.917] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-09 17:45:17.917] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-09 17:45:41.460] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-09 17:46:04.775] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-09 17:46:29.133] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-09 17:46:53.838] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-09 17:47:17.572] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-09 17:47:41.090] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-09 17:48:04.817] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-09 17:48:28.408] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-09 17:48:51.723] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-09 17:49:15.974] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-09 17:49:15.993] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-09 17:49:47.077] [jointLog] [info] iteration = 100 | max rel diff. = 14.0568
[2023-09-09 17:50:21.995] [jointLog] [info] iteration = 200 | max rel diff. = 20.8159
[2023-09-09 17:50:56.371] [jointLog] [info] iteration = 300 | max rel diff. = 14.8163
[2023-09-09 17:51:30.759] [jointLog] [info] iteration = 400 | max rel diff. = 8.44759
[2023-09-09 17:52:04.940] [jointLog] [info] iteration = 500 | max rel diff. = 0.745522
[2023-09-09 17:52:39.623] [jointLog] [info] iteration = 600 | max rel diff. = 2.37918
[2023-09-09 17:53:13.663] [jointLog] [info] iteration = 700 | max rel diff. = 1.91157
[2023-09-09 17:53:47.413] [jointLog] [info] iteration = 800 | max rel diff. = 6.1797
[2023-09-09 17:54:21.243] [jointLog] [info] iteration = 900 | max rel diff. = 0.248555
[2023-09-09 17:54:55.014] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.292938
[2023-09-09 17:55:28.866] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.919161
[2023-09-09 17:56:02.522] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.740805
[2023-09-09 17:56:36.692] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0342011
[2023-09-09 17:57:10.707] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0221156
[2023-09-09 17:57:44.247] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0907793
[2023-09-09 17:57:51.329] [jointLog] [info] iteration = 1,522 | max rel diff. = 0.0088383
[2023-09-09 17:57:52.962] [jointLog] [info] Finished optimizer
[2023-09-09 17:57:52.962] [jointLog] [info] writing output