[2022-02-10 18:15:13.723] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-02-10 18:15:13.723] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-02-10 18:15:13.723] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-02-10 18:15:13.723] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2022-02-10 18:15:13.723] [jointLog] [info] parsing read library format
[2022-02-10 18:15:13.723] [jointLog] [info] There is 1 library.
[2022-02-10 18:15:13.845] [jointLog] [info] Loading pufferfish index
[2022-02-10 18:15:13.845] [jointLog] [info] Loading dense pufferfish index.
[2022-02-10 18:16:59.179] [jointLog] [info] done
[2022-02-10 18:16:59.179] [jointLog] [info] Index contained 5,382,683 targets
[2022-02-10 18:17:54.809] [jointLog] [info] Number of decoys : 194
[2022-02-10 18:17:54.809] [jointLog] [info] First decoy index : 5,185,409 
[2022-02-10 18:17:56.479] [jointLog] [info] Automatically detected most likely library type as IU
[2022-02-10 18:20:42.424] [fileLog] [info] 
At end of round 0
==================
Observed 18948257 total fragments (18948257 in most recent round)

[2022-02-10 18:20:42.423] [jointLog] [info] Computed 190,721 rich equivalence classes for further processing
[2022-02-10 18:20:42.423] [jointLog] [info] Counted 17,916,481 total reads in the equivalence classes 
[2022-02-10 18:20:42.433] [jointLog] [info] Number of mappings discarded because of alignment score : 7,187,782
[2022-02-10 18:20:42.433] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 960,507
[2022-02-10 18:20:42.433] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 273,400
[2022-02-10 18:20:42.433] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 80,008
[2022-02-10 18:20:42.433] [jointLog] [info] Mapping rate = 94.5548%

[2022-02-10 18:20:42.433] [jointLog] [info] finished quantifyLibrary()
[2022-02-10 18:20:42.433] [jointLog] [info] Starting optimizer
[2022-02-10 18:20:47.240] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-02-10 18:20:47.579] [jointLog] [info] iteration = 0 | max rel diff. = 266.355
[2022-02-10 18:20:50.876] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-02-10 18:24:28.430] [jointLog] [info] Computed expected counts (for bias correction)
[2022-02-10 18:24:28.431] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-02-10 18:24:47.230] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-02-10 18:25:05.982] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-02-10 18:25:24.974] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-02-10 18:25:45.489] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-02-10 18:26:04.016] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-02-10 18:26:24.376] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-02-10 18:26:44.091] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-02-10 18:27:02.993] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-02-10 18:27:21.553] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-02-10 18:27:40.607] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-02-10 18:27:40.607] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-02-10 18:28:10.225] [jointLog] [info] iteration = 100 | max rel diff. = 7.13384
[2022-02-10 18:28:42.290] [jointLog] [info] iteration = 200 | max rel diff. = 5.15804
[2022-02-10 18:29:14.251] [jointLog] [info] iteration = 300 | max rel diff. = 0.178936
[2022-02-10 18:29:48.639] [jointLog] [info] iteration = 400 | max rel diff. = 0.39647
[2022-02-10 18:30:20.835] [jointLog] [info] iteration = 500 | max rel diff. = 0.300319
[2022-02-10 18:30:53.033] [jointLog] [info] iteration = 600 | max rel diff. = 0.173163
[2022-02-10 18:31:25.394] [jointLog] [info] iteration = 700 | max rel diff. = 0.178487
[2022-02-10 18:31:57.707] [jointLog] [info] iteration = 800 | max rel diff. = 0.26133
[2022-02-10 18:32:02.484] [jointLog] [info] iteration = 816 | max rel diff. = 0.00384919
[2022-02-10 18:32:04.708] [jointLog] [info] Finished optimizer
[2022-02-10 18:32:04.708] [jointLog] [info] writing output