[2022-01-03 13:12:45.211] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-01-03 13:12:45.211] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-01-03 13:12:45.211] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-01-03 13:12:45.211] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2022-01-03 13:12:45.211] [jointLog] [info] parsing read library format
[2022-01-03 13:12:45.211] [jointLog] [info] There is 1 library.
[2022-01-03 13:12:45.272] [jointLog] [info] Loading pufferfish index
[2022-01-03 13:12:45.273] [jointLog] [info] Loading dense pufferfish index.
[2022-01-03 13:14:16.156] [jointLog] [info] done
[2022-01-03 13:14:16.156] [jointLog] [info] Index contained 5,382,683 targets
[2022-01-03 13:14:58.293] [jointLog] [info] Number of decoys : 194
[2022-01-03 13:14:58.293] [jointLog] [info] First decoy index : 5,185,409 
[2022-01-03 13:15:00.104] [jointLog] [info] Automatically detected most likely library type as IU
[2022-01-03 13:22:27.328] [fileLog] [info] 
At end of round 0
==================
Observed 23845932 total fragments (23845932 in most recent round)

[2022-01-03 13:22:27.327] [jointLog] [info] Computed 251,269 rich equivalence classes for further processing
[2022-01-03 13:22:27.327] [jointLog] [info] Counted 14,606,452 total reads in the equivalence classes 
[2022-01-03 13:22:27.336] [jointLog] [info] Number of mappings discarded because of alignment score : 23,619,548
[2022-01-03 13:22:27.336] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,038,826
[2022-01-03 13:22:27.336] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 364,264
[2022-01-03 13:22:27.336] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 385,143
[2022-01-03 13:22:27.336] [jointLog] [info] Mapping rate = 61.2534%

[2022-01-03 13:22:27.336] [jointLog] [info] finished quantifyLibrary()
[2022-01-03 13:22:27.336] [jointLog] [info] Starting optimizer
[2022-01-03 13:22:29.706] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-01-03 13:22:30.021] [jointLog] [info] iteration = 0 | max rel diff. = 272.289
[2022-01-03 13:22:33.207] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-01-03 13:26:49.946] [jointLog] [info] Computed expected counts (for bias correction)
[2022-01-03 13:26:49.947] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-01-03 13:27:11.209] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-01-03 13:27:32.370] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-01-03 13:27:53.685] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-01-03 13:28:15.514] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-01-03 13:28:35.573] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-01-03 13:28:56.050] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-01-03 13:29:17.831] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-01-03 13:29:39.366] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-01-03 13:30:01.465] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-01-03 13:30:22.210] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-01-03 13:30:51.050] [jointLog] [info] iteration = 100 | max rel diff. = 16.441
[2022-01-03 13:31:22.707] [jointLog] [info] iteration = 200 | max rel diff. = 6.66661
[2022-01-03 13:31:54.189] [jointLog] [info] iteration = 300 | max rel diff. = 1.71228
[2022-01-03 13:32:25.325] [jointLog] [info] iteration = 400 | max rel diff. = 0.520448
[2022-01-03 13:32:56.256] [jointLog] [info] iteration = 500 | max rel diff. = 5.40764
[2022-01-03 13:33:27.122] [jointLog] [info] iteration = 600 | max rel diff. = 0.160024
[2022-01-03 13:33:58.193] [jointLog] [info] iteration = 700 | max rel diff. = 0.530916
[2022-01-03 13:34:29.713] [jointLog] [info] iteration = 800 | max rel diff. = 0.162965
[2022-01-03 13:35:01.270] [jointLog] [info] iteration = 900 | max rel diff. = 0.357968
[2022-01-03 13:35:32.152] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.143452
[2022-01-03 13:35:58.013] [jointLog] [info] iteration = 1,084 | max rel diff. = 0.00929588
[2022-01-03 13:35:59.086] [jointLog] [info] Finished optimizer
[2022-01-03 13:35:59.086] [jointLog] [info] writing output