[2022-12-20 23:56:10.482] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:56:10.482] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:56:10.482] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:56:10.482] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:56:10.482] [jointLog] [info] parsing read library format
[2022-12-20 23:56:10.482] [jointLog] [info] There is 1 library.
[2022-12-20 23:56:10.482] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:56:10.483] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:56:28.645] [jointLog] [info] done
[2022-12-20 23:56:28.680] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:56:28.961] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:56:28.961] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:56:29.647] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-21 00:00:21.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:00:21.275] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-12-21 00:00:21.295] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:00:21.351] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:00:21.390] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:00:21.567] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:00:21.605] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:00:21.638] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:00:21.898] [fileLog] [info] 
At end of round 0
==================
Observed 18915393 total fragments (18915393 in most recent round)

[2022-12-21 00:00:21.897] [jointLog] [info] Computed 263,081 rich equivalence classes for further processing
[2022-12-21 00:00:21.897] [jointLog] [info] Counted 13,715,157 total reads in the equivalence classes 
[2022-12-21 00:00:21.902] [jointLog] [info] Number of mappings discarded because of alignment score : 40,918,689
[2022-12-21 00:00:21.902] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,433,201
[2022-12-21 00:00:21.902] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 290,565
[2022-12-21 00:00:21.902] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,599,992
[2022-12-21 00:00:21.902] [jointLog] [info] Mapping rate = 72.5079%

[2022-12-21 00:00:21.902] [jointLog] [info] finished quantifyLibrary()
[2022-12-21 00:00:21.933] [jointLog] [info] Starting optimizer
[2022-12-21 00:00:22.848] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-21 00:00:22.862] [jointLog] [info] iteration = 0 | max rel diff. = 6676.68
[2022-12-21 00:00:23.003] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-21 00:00:24.328] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-21 00:00:24.328] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-21 00:00:25.166] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-21 00:00:26.074] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-21 00:00:26.963] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-21 00:00:27.907] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-21 00:00:28.733] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-21 00:00:29.471] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-21 00:00:30.324] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-21 00:00:31.146] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-21 00:00:31.971] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-21 00:00:32.853] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-21 00:00:34.193] [jointLog] [info] iteration = 100 | max rel diff. = 12.5212
[2022-12-21 00:00:35.610] [jointLog] [info] iteration = 200 | max rel diff. = 17.2549
[2022-12-21 00:00:37.136] [jointLog] [info] iteration = 300 | max rel diff. = 1.82758
[2022-12-21 00:00:38.619] [jointLog] [info] iteration = 400 | max rel diff. = 0.340684
[2022-12-21 00:00:40.024] [jointLog] [info] iteration = 500 | max rel diff. = 0.156413
[2022-12-21 00:00:41.441] [jointLog] [info] iteration = 600 | max rel diff. = 0.0447472
[2022-12-21 00:00:42.818] [jointLog] [info] iteration = 700 | max rel diff. = 0.417975
[2022-12-21 00:00:44.012] [jointLog] [info] iteration = 800 | max rel diff. = 0.100064
[2022-12-21 00:00:45.260] [jointLog] [info] iteration = 900 | max rel diff. = 0.12659
[2022-12-21 00:00:46.615] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.475994
[2022-12-21 00:00:46.657] [jointLog] [info] iteration = 1,004 | max rel diff. = 0.00608694
[2022-12-21 00:00:46.676] [jointLog] [info] Finished optimizer
[2022-12-21 00:00:46.676] [jointLog] [info] writing output