[2021-02-20 03:47:08.677] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-02-20 03:47:08.677] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-02-20 03:47:08.677] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-02-20 03:47:08.677] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-02-20 03:47:08.678] [jointLog] [info] parsing read library format
[2021-02-20 03:47:08.678] [jointLog] [info] There is 1 library.
[2021-02-20 03:47:08.809] [jointLog] [info] Loading pufferfish index
[2021-02-20 03:47:08.810] [jointLog] [info] Loading dense pufferfish index.
[2021-02-20 03:48:57.650] [jointLog] [info] done
[2021-02-20 03:48:57.650] [jointLog] [info] Index contained 5,382,683 targets
[2021-02-20 03:49:52.825] [jointLog] [info] Number of decoys : 194
[2021-02-20 03:49:52.826] [jointLog] [info] First decoy index : 5,185,409 
[2021-02-20 03:49:55.829] [jointLog] [info] Automatically detected most likely library type as IU
[2021-02-20 04:18:38.021] [fileLog] [info] 
At end of round 0
==================
Observed 215755589 total fragments (215755589 in most recent round)

[2021-02-20 04:18:38.021] [jointLog] [info] Computed 909,702 rich equivalence classes for further processing
[2021-02-20 04:18:38.021] [jointLog] [info] Counted 200,851,244 total reads in the equivalence classes 
[2021-02-20 04:18:38.031] [jointLog] [info] Number of mappings discarded because of alignment score : 73,694,783
[2021-02-20 04:18:38.031] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,991,238
[2021-02-20 04:18:38.031] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 3,293,259
[2021-02-20 04:18:38.031] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,009,027
[2021-02-20 04:18:38.031] [jointLog] [info] Mapping rate = 93.092%

[2021-02-20 04:18:38.031] [jointLog] [info] finished quantifyLibrary()
[2021-02-20 04:18:38.031] [jointLog] [info] Starting optimizer
[2021-02-20 04:18:42.899] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-02-20 04:18:43.277] [jointLog] [info] iteration = 0 | max rel diff. = 190.246
[2021-02-20 04:18:47.138] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-02-20 04:27:27.294] [jointLog] [info] Computed expected counts (for bias correction)
[2021-02-20 04:27:27.294] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-02-20 04:28:08.424] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-02-20 04:28:48.066] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-02-20 04:29:29.659] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-02-20 04:30:10.890] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-02-20 04:30:49.712] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-02-20 04:31:29.733] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-02-20 04:32:10.256] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-02-20 04:32:49.744] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-02-20 04:33:31.306] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-02-20 04:34:10.778] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-02-20 04:34:10.786] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-02-20 04:34:47.291] [jointLog] [info] iteration = 100 | max rel diff. = 10.5376
[2021-02-20 04:35:26.665] [jointLog] [info] iteration = 200 | max rel diff. = 9.12297
[2021-02-20 04:36:05.653] [jointLog] [info] iteration = 300 | max rel diff. = 1.64906
[2021-02-20 04:36:44.674] [jointLog] [info] iteration = 400 | max rel diff. = 1.12308
[2021-02-20 04:37:23.811] [jointLog] [info] iteration = 500 | max rel diff. = 1.10752
[2021-02-20 04:38:02.944] [jointLog] [info] iteration = 600 | max rel diff. = 7.72143
[2021-02-20 04:38:41.748] [jointLog] [info] iteration = 700 | max rel diff. = 0.222511
[2021-02-20 04:39:19.939] [jointLog] [info] iteration = 800 | max rel diff. = 0.160794
[2021-02-20 04:39:58.025] [jointLog] [info] iteration = 900 | max rel diff. = 0.370601
[2021-02-20 04:40:37.232] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.149831
[2021-02-20 04:41:16.377] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0369805
[2021-02-20 04:41:55.427] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.118931
[2021-02-20 04:42:34.472] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.186039
[2021-02-20 04:42:43.364] [jointLog] [info] iteration = 1,324 | max rel diff. = 0.00840633
[2021-02-20 04:42:45.210] [jointLog] [info] Finished optimizer
[2021-02-20 04:42:45.210] [jointLog] [info] writing output