[2023-10-04 00:12:57.497] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 00:12:57.497] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 00:12:57.497] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 00:12:57.497] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 00:12:57.497] [jointLog] [info] parsing read library format
[2023-10-04 00:12:57.497] [jointLog] [info] There is 1 library.
[2023-10-04 00:12:57.497] [jointLog] [info] Loading pufferfish index
[2023-10-04 00:12:57.497] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 00:14:14.308] [jointLog] [info] done
[2023-10-04 00:14:14.467] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 00:14:55.569] [jointLog] [info] Number of decoys : 194
[2023-10-04 00:14:55.570] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 00:14:57.660] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 00:14:58.373] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 00:15:43.290] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-04 00:15:43.313] [jointLog] [info] Thread saw mini-batch with a maximum of 4.34% zero probability fragments
[2023-10-04 00:15:43.350] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2023-10-04 00:15:43.380] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-10-04 00:15:43.536] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-04 00:15:43.556] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2023-10-04 00:15:43.586] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-10-04 00:15:43.986] [fileLog] [info] 
At end of round 0
==================
Observed 3449751 total fragments (3449751 in most recent round)

[2023-10-04 00:15:43.798] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-10-04 00:15:43.985] [jointLog] [info] Computed 77,544 rich equivalence classes for further processing
[2023-10-04 00:15:43.985] [jointLog] [info] Counted 2,634,730 total reads in the equivalence classes 
[2023-10-04 00:15:43.993] [jointLog] [info] Number of mappings discarded because of alignment score : 41,857,887
[2023-10-04 00:15:43.993] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 244,239
[2023-10-04 00:15:43.993] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 85,431
[2023-10-04 00:15:43.993] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 00:15:45.192] [jointLog] [warning] Only 2634730 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 00:15:45.192] [jointLog] [info] Mapping rate = 76.3745%

[2023-10-04 00:15:45.192] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 00:15:45.193] [jointLog] [info] Starting optimizer
[2023-10-04 00:15:51.091] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 00:15:51.450] [jointLog] [info] iteration = 0 | max rel diff. = 48.0427
[2023-10-04 00:15:54.947] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 00:16:49.402] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 00:16:49.403] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 00:16:54.493] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 00:16:59.332] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 00:17:03.998] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 00:17:09.110] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 00:17:14.200] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 00:17:19.071] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 00:17:23.869] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 00:17:28.983] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 00:17:33.935] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 00:17:38.670] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 00:18:09.491] [jointLog] [info] iteration = 100 | max rel diff. = 9.99072
[2023-10-04 00:18:42.722] [jointLog] [info] iteration = 200 | max rel diff. = 0.465233
[2023-10-04 00:19:15.517] [jointLog] [info] iteration = 300 | max rel diff. = 3.0072
[2023-10-04 00:19:48.051] [jointLog] [info] iteration = 400 | max rel diff. = 0.127825
[2023-10-04 00:20:20.941] [jointLog] [info] iteration = 500 | max rel diff. = 0.561406
[2023-10-04 00:20:53.785] [jointLog] [info] iteration = 600 | max rel diff. = 0.023964
[2023-10-04 00:21:26.879] [jointLog] [info] iteration = 700 | max rel diff. = 0.015148
[2023-10-04 00:21:59.921] [jointLog] [info] iteration = 800 | max rel diff. = 0.268087
[2023-10-04 00:22:32.703] [jointLog] [info] iteration = 900 | max rel diff. = 0.0506572
[2023-10-04 00:22:49.884] [jointLog] [info] iteration = 955 | max rel diff. = 0.00836114
[2023-10-04 00:22:52.120] [jointLog] [info] Finished optimizer
[2023-10-04 00:22:52.120] [jointLog] [info] writing output