[2023-10-03 23:28:31.385] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 23:28:31.385] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 23:28:31.385] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 23:28:31.385] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 23:28:31.385] [jointLog] [info] parsing read library format
[2023-10-03 23:28:31.386] [jointLog] [info] There is 1 library.
[2023-10-03 23:28:31.386] [jointLog] [info] Loading pufferfish index
[2023-10-03 23:28:31.386] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 23:29:51.046] [jointLog] [info] done
[2023-10-03 23:29:51.203] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 23:30:30.895] [jointLog] [info] Number of decoys : 194
[2023-10-03 23:30:30.895] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 23:30:32.901] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 23:30:33.641] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 23:31:10.573] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 23:31:10.609] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 23:31:10.637] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-03 23:31:10.912] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-03 23:31:10.930] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 23:31:10.942] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-03 23:31:11.061] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-10-03 23:31:11.069] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 23:31:11.254] [jointLog] [info] Computed 72,139 rich equivalence classes for further processing
[2023-10-03 23:31:11.254] [jointLog] [info] Counted 2,268,448 total reads in the equivalence classes 
[2023-10-03 23:31:11.262] [jointLog] [info] Number of mappings discarded because of alignment score : 46,774,224
[2023-10-03 23:31:11.262] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 233,948
[2023-10-03 23:31:11.262] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 61,283
[2023-10-03 23:31:11.262] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 23:31:11.255] [fileLog] [info] 
At end of round 0
==================
Observed 2987799 total fragments (2987799 in most recent round)

[2023-10-03 23:31:12.431] [jointLog] [warning] Only 2268448 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 23:31:12.431] [jointLog] [info] Mapping rate = 75.9237%

[2023-10-03 23:31:12.431] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 23:31:12.432] [jointLog] [info] Starting optimizer
[2023-10-03 23:31:17.050] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 23:31:17.390] [jointLog] [info] iteration = 0 | max rel diff. = 42.6994
[2023-10-03 23:31:20.760] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 23:32:10.746] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 23:32:10.746] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 23:32:15.341] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 23:32:20.142] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 23:32:24.704] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 23:32:29.644] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 23:32:34.317] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 23:32:38.918] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 23:32:43.168] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 23:32:47.955] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 23:32:53.028] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 23:32:57.778] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 23:33:28.605] [jointLog] [info] iteration = 100 | max rel diff. = 3.36834
[2023-10-03 23:34:02.466] [jointLog] [info] iteration = 200 | max rel diff. = 0.269461
[2023-10-03 23:34:36.121] [jointLog] [info] iteration = 300 | max rel diff. = 1.00474
[2023-10-03 23:35:09.574] [jointLog] [info] iteration = 400 | max rel diff. = 0.371421
[2023-10-03 23:35:42.570] [jointLog] [info] iteration = 500 | max rel diff. = 0.0354957
[2023-10-03 23:36:15.235] [jointLog] [info] iteration = 600 | max rel diff. = 0.0193062
[2023-10-03 23:36:46.767] [jointLog] [info] iteration = 700 | max rel diff. = 0.0430551
[2023-10-03 23:37:18.246] [jointLog] [info] iteration = 800 | max rel diff. = 0.0388248
[2023-10-03 23:37:49.904] [jointLog] [info] iteration = 900 | max rel diff. = 0.0264315
[2023-10-03 23:38:20.255] [jointLog] [info] iteration = 994 | max rel diff. = 0.0084941
[2023-10-03 23:38:22.397] [jointLog] [info] Finished optimizer
[2023-10-03 23:38:22.397] [jointLog] [info] writing output