[2022-02-10 06:32:10.410] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-02-10 06:32:10.410] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-02-10 06:32:10.410] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-02-10 06:32:10.410] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2022-02-10 06:32:10.410] [jointLog] [info] parsing read library format
[2022-02-10 06:32:10.410] [jointLog] [info] There is 1 library.
[2022-02-10 06:32:10.522] [jointLog] [info] Loading pufferfish index
[2022-02-10 06:32:10.522] [jointLog] [info] Loading dense pufferfish index.
[2022-02-10 06:34:13.190] [jointLog] [info] done
[2022-02-10 06:34:13.190] [jointLog] [info] Index contained 5,382,683 targets
[2022-02-10 06:35:09.143] [jointLog] [info] Number of decoys : 194
[2022-02-10 06:35:09.143] [jointLog] [info] First decoy index : 5,185,409 
[2022-02-10 06:35:12.354] [jointLog] [info] Automatically detected most likely library type as IU
[2022-02-10 06:40:54.456] [fileLog] [info] 
At end of round 0
==================
Observed 24076318 total fragments (24076318 in most recent round)

[2022-02-10 06:40:54.455] [jointLog] [info] Computed 253,559 rich equivalence classes for further processing
[2022-02-10 06:40:54.455] [jointLog] [info] Counted 22,121,443 total reads in the equivalence classes 
[2022-02-10 06:40:54.468] [jointLog] [info] Number of mappings discarded because of alignment score : 9,947,472
[2022-02-10 06:40:54.468] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,787,782
[2022-02-10 06:40:54.468] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 577,339
[2022-02-10 06:40:54.468] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 571,967
[2022-02-10 06:40:54.468] [jointLog] [info] Mapping rate = 91.8805%

[2022-02-10 06:40:54.468] [jointLog] [info] finished quantifyLibrary()
[2022-02-10 06:40:54.469] [jointLog] [info] Starting optimizer
[2022-02-10 06:41:04.938] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-02-10 06:41:05.271] [jointLog] [info] iteration = 0 | max rel diff. = 286.664
[2022-02-10 06:41:08.644] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-02-10 06:44:56.258] [jointLog] [info] Computed expected counts (for bias correction)
[2022-02-10 06:44:56.259] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-02-10 06:45:14.649] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-02-10 06:45:32.889] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-02-10 06:45:51.427] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-02-10 06:46:10.804] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-02-10 06:46:30.258] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-02-10 06:46:48.480] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-02-10 06:47:07.040] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-02-10 06:47:25.537] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-02-10 06:47:49.461] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-02-10 06:48:08.946] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-02-10 06:48:08.985] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-02-10 06:48:37.463] [jointLog] [info] iteration = 100 | max rel diff. = 9.79962
[2022-02-10 06:49:08.525] [jointLog] [info] iteration = 200 | max rel diff. = 2.39521
[2022-02-10 06:49:40.439] [jointLog] [info] iteration = 300 | max rel diff. = 1.49404
[2022-02-10 06:50:13.358] [jointLog] [info] iteration = 400 | max rel diff. = 0.166421
[2022-02-10 06:50:46.796] [jointLog] [info] iteration = 500 | max rel diff. = 8.24606
[2022-02-10 06:51:20.572] [jointLog] [info] iteration = 600 | max rel diff. = 1.3386
[2022-02-10 06:51:53.750] [jointLog] [info] iteration = 700 | max rel diff. = 0.0759597
[2022-02-10 06:52:27.218] [jointLog] [info] iteration = 800 | max rel diff. = 0.0612484
[2022-02-10 06:53:00.850] [jointLog] [info] iteration = 900 | max rel diff. = 0.0744855
[2022-02-10 06:53:33.431] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.081634
[2022-02-10 06:53:42.705] [jointLog] [info] iteration = 1,029 | max rel diff. = 0.006981
[2022-02-10 06:53:44.305] [jointLog] [info] Finished optimizer
[2022-02-10 06:53:44.305] [jointLog] [info] writing output