[2023-10-04 13:27:29.093] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 13:27:29.093] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 13:27:29.093] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 13:27:29.093] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 13:27:29.093] [jointLog] [info] parsing read library format
[2023-10-04 13:27:29.093] [jointLog] [info] There is 1 library.
[2023-10-04 13:27:29.094] [jointLog] [info] Loading pufferfish index
[2023-10-04 13:27:29.094] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 13:28:42.802] [jointLog] [info] done
[2023-10-04 13:28:42.926] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 13:29:20.320] [jointLog] [info] Number of decoys : 194
[2023-10-04 13:29:20.320] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 13:29:22.052] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 13:29:23.106] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 13:30:03.226] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 13:30:03.228] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 13:30:03.312] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-04 13:30:03.438] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-10-04 13:30:03.505] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-10-04 13:30:03.577] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 13:30:03.630] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 13:30:03.701] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 13:30:03.849] [jointLog] [info] Computed 75,589 rich equivalence classes for further processing
[2023-10-04 13:30:03.849] [jointLog] [info] Counted 1,798,803 total reads in the equivalence classes 
[2023-10-04 13:30:03.856] [jointLog] [info] Number of mappings discarded because of alignment score : 52,092,750
[2023-10-04 13:30:03.856] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 263,916
[2023-10-04 13:30:03.856] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 64,263
[2023-10-04 13:30:03.856] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 13:30:03.850] [fileLog] [info] 
At end of round 0
==================
Observed 2590636 total fragments (2590636 in most recent round)

[2023-10-04 13:30:04.763] [jointLog] [warning] Only 1798803 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 13:30:04.763] [jointLog] [info] Mapping rate = 69.4348%

[2023-10-04 13:30:04.763] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 13:30:04.764] [jointLog] [info] Starting optimizer
[2023-10-04 13:30:08.414] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 13:30:08.721] [jointLog] [info] iteration = 0 | max rel diff. = 38.2328
[2023-10-04 13:30:11.979] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 13:31:04.232] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 13:31:04.233] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 13:31:08.958] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 13:31:13.481] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 13:31:18.347] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 13:31:22.998] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 13:31:27.924] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 13:31:32.911] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 13:31:37.828] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 13:31:42.788] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 13:31:47.923] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 13:31:52.536] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 13:31:52.538] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 13:32:21.315] [jointLog] [info] iteration = 100 | max rel diff. = 2.74603
[2023-10-04 13:32:52.681] [jointLog] [info] iteration = 200 | max rel diff. = 8.2122
[2023-10-04 13:33:24.413] [jointLog] [info] iteration = 300 | max rel diff. = 17.6863
[2023-10-04 13:33:59.598] [jointLog] [info] iteration = 400 | max rel diff. = 0.109974
[2023-10-04 13:34:31.750] [jointLog] [info] iteration = 500 | max rel diff. = 0.349342
[2023-10-04 13:35:03.810] [jointLog] [info] iteration = 600 | max rel diff. = 0.0341518
[2023-10-04 13:35:35.715] [jointLog] [info] iteration = 700 | max rel diff. = 0.0213493
[2023-10-04 13:36:07.561] [jointLog] [info] iteration = 800 | max rel diff. = 1.52945
[2023-10-04 13:36:27.550] [jointLog] [info] iteration = 860 | max rel diff. = 0.0036664
[2023-10-04 13:36:29.438] [jointLog] [info] Finished optimizer
[2023-10-04 13:36:29.438] [jointLog] [info] writing output