[2021-02-19 14:25:12.583] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-02-19 14:25:12.583] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-02-19 14:25:12.583] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-02-19 14:25:12.583] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-02-19 14:25:12.583] [jointLog] [info] parsing read library format
[2021-02-19 14:25:12.583] [jointLog] [info] There is 1 library.
[2021-02-19 14:25:12.703] [jointLog] [info] Loading pufferfish index
[2021-02-19 14:25:12.703] [jointLog] [info] Loading dense pufferfish index.
[2021-02-19 14:27:14.613] [jointLog] [info] done
[2021-02-19 14:27:14.613] [jointLog] [info] Index contained 5,382,683 targets
[2021-02-19 14:28:07.935] [jointLog] [info] Number of decoys : 194
[2021-02-19 14:28:07.935] [jointLog] [info] First decoy index : 5,185,409 
[2021-02-19 14:28:11.918] [jointLog] [info] Automatically detected most likely library type as ISF
[2021-02-19 14:29:57.936] [jointLog] [info] Thread saw mini-batch with a maximum of 13.82% zero probability fragments
[2021-02-19 14:29:57.988] [jointLog] [info] Thread saw mini-batch with a maximum of 13.90% zero probability fragments
[2021-02-19 14:29:58.035] [jointLog] [info] Thread saw mini-batch with a maximum of 13.78% zero probability fragments
[2021-02-19 14:29:58.053] [jointLog] [info] Thread saw mini-batch with a maximum of 13.84% zero probability fragments
[2021-02-19 14:29:58.087] [jointLog] [info] Thread saw mini-batch with a maximum of 14.04% zero probability fragments
[2021-02-19 14:29:58.090] [jointLog] [info] Thread saw mini-batch with a maximum of 14.00% zero probability fragments
[2021-02-19 14:29:58.119] [jointLog] [info] Thread saw mini-batch with a maximum of 14.00% zero probability fragments
[2021-02-19 14:29:58.200] [jointLog] [info] Thread saw mini-batch with a maximum of 14.10% zero probability fragments
[2021-02-19 14:29:58.603] [fileLog] [info] 
At end of round 0
==================
Observed 10091853 total fragments (10091853 in most recent round)

[2021-02-19 14:29:58.602] [jointLog] [info] Computed 384,217 rich equivalence classes for further processing
[2021-02-19 14:29:58.602] [jointLog] [info] Counted 6,940,651 total reads in the equivalence classes 
[2021-02-19 14:29:58.614] [jointLog] [info] Number of mappings discarded because of alignment score : 17,372,292
[2021-02-19 14:29:58.614] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 987,209
[2021-02-19 14:29:58.614] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 464,323
[2021-02-19 14:29:58.614] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 595,090
[2021-02-19 14:29:58.614] [jointLog] [info] Mapping rate = 68.7748%

[2021-02-19 14:29:58.614] [jointLog] [info] finished quantifyLibrary()
[2021-02-19 14:29:58.615] [jointLog] [info] Starting optimizer
[2021-02-19 14:30:04.032] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-02-19 14:30:04.381] [jointLog] [info] iteration = 0 | max rel diff. = 165.353
[2021-02-19 14:30:07.981] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-02-19 14:36:31.985] [jointLog] [info] Computed expected counts (for bias correction)
[2021-02-19 14:36:31.986] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-02-19 14:37:01.965] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-02-19 14:37:31.948] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-02-19 14:38:01.782] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-02-19 14:38:32.526] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-02-19 14:39:02.636] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-02-19 14:39:32.953] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-02-19 14:40:03.545] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-02-19 14:40:33.212] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-02-19 14:41:10.877] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-02-19 14:41:41.421] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-02-19 14:42:18.460] [jointLog] [info] iteration = 100 | max rel diff. = 7.43437
[2021-02-19 14:42:53.753] [jointLog] [info] iteration = 200 | max rel diff. = 4.56407
[2021-02-19 14:43:28.444] [jointLog] [info] iteration = 300 | max rel diff. = 5.99222
[2021-02-19 14:44:03.134] [jointLog] [info] iteration = 400 | max rel diff. = 1.50758
[2021-02-19 14:44:38.954] [jointLog] [info] iteration = 500 | max rel diff. = 0.512821
[2021-02-19 14:45:14.707] [jointLog] [info] iteration = 600 | max rel diff. = 0.17465
[2021-02-19 14:45:50.366] [jointLog] [info] iteration = 700 | max rel diff. = 0.122172
[2021-02-19 14:46:26.127] [jointLog] [info] iteration = 800 | max rel diff. = 0.429144
[2021-02-19 14:47:01.271] [jointLog] [info] iteration = 900 | max rel diff. = 1.0831
[2021-02-19 14:47:33.354] [jointLog] [info] iteration = 993 | max rel diff. = 0.00553332
[2021-02-19 14:47:35.472] [jointLog] [info] Finished optimizer
[2021-02-19 14:47:35.472] [jointLog] [info] writing output