[2022-12-21 00:04:56.265] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-21 00:04:56.265] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-21 00:04:56.265] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-21 00:04:56.265] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-21 00:04:56.265] [jointLog] [info] parsing read library format
[2022-12-21 00:04:56.265] [jointLog] [info] There is 1 library.
[2022-12-21 00:04:56.266] [jointLog] [info] Loading pufferfish index
[2022-12-21 00:04:56.266] [jointLog] [info] Loading dense pufferfish index.
[2022-12-21 00:05:15.561] [jointLog] [info] done
[2022-12-21 00:05:15.603] [jointLog] [info] Index contained 147,889 targets
[2022-12-21 00:05:15.904] [jointLog] [info] Number of decoys : 61
[2022-12-21 00:05:15.904] [jointLog] [info] First decoy index : 147,789 
[2022-12-21 00:05:16.759] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-21 00:08:09.664] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:08:09.749] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:08:09.754] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:08:09.793] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:08:09.814] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:08:09.814] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:08:09.846] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:08:09.850] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-21 00:08:10.042] [jointLog] [info] Computed 275,687 rich equivalence classes for further processing
[2022-12-21 00:08:10.042] [jointLog] [info] Counted 15,674,553 total reads in the equivalence classes 
[2022-12-21 00:08:10.046] [jointLog] [info] Number of mappings discarded because of alignment score : 32,409,685
[2022-12-21 00:08:10.046] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,653,691
[2022-12-21 00:08:10.046] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 400,436
[2022-12-21 00:08:10.046] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,137,638
[2022-12-21 00:08:10.046] [jointLog] [info] Mapping rate = 77.9701%

[2022-12-21 00:08:10.046] [jointLog] [info] finished quantifyLibrary()
[2022-12-21 00:08:10.046] [jointLog] [info] Starting optimizer
[2022-12-21 00:08:10.132] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-21 00:08:10.148] [jointLog] [info] iteration = 0 | max rel diff. = 7253.76
[2022-12-21 00:08:10.280] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-21 00:08:10.043] [fileLog] [info] 
At end of round 0
==================
Observed 20103287 total fragments (20103287 in most recent round)

[2022-12-21 00:08:11.060] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-21 00:08:11.060] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-21 00:08:11.537] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-21 00:08:12.038] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-21 00:08:12.543] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-21 00:08:13.004] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-21 00:08:13.443] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-21 00:08:13.930] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-21 00:08:14.407] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-21 00:08:14.930] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-21 00:08:15.406] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-21 00:08:15.799] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-21 00:08:15.801] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-21 00:08:16.863] [jointLog] [info] iteration = 100 | max rel diff. = 15.8647
[2022-12-21 00:08:18.051] [jointLog] [info] iteration = 200 | max rel diff. = 11.9127
[2022-12-21 00:08:19.238] [jointLog] [info] iteration = 300 | max rel diff. = 14.8339
[2022-12-21 00:08:20.424] [jointLog] [info] iteration = 400 | max rel diff. = 0.638936
[2022-12-21 00:08:21.609] [jointLog] [info] iteration = 500 | max rel diff. = 0.320806
[2022-12-21 00:08:22.798] [jointLog] [info] iteration = 600 | max rel diff. = 0.0891707
[2022-12-21 00:08:23.985] [jointLog] [info] iteration = 700 | max rel diff. = 0.852213
[2022-12-21 00:08:25.168] [jointLog] [info] iteration = 800 | max rel diff. = 0.404675
[2022-12-21 00:08:26.355] [jointLog] [info] iteration = 900 | max rel diff. = 0.0374482
[2022-12-21 00:08:27.560] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0818773
[2022-12-21 00:08:28.745] [jointLog] [info] iteration = 1,100 | max rel diff. = 16.1252
[2022-12-21 00:08:29.938] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0516453
[2022-12-21 00:08:31.128] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0247122
[2022-12-21 00:08:31.498] [jointLog] [info] iteration = 1,332 | max rel diff. = 0.003442
[2022-12-21 00:08:31.516] [jointLog] [info] Finished optimizer
[2022-12-21 00:08:31.516] [jointLog] [info] writing output