[2023-10-03 10:14:42.887] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 10:14:42.887] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 10:14:42.887] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 10:14:42.887] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 10:14:42.887] [jointLog] [info] parsing read library format
[2023-10-03 10:14:42.887] [jointLog] [info] There is 1 library.
[2023-10-03 10:14:42.887] [jointLog] [info] Loading pufferfish index
[2023-10-03 10:14:42.887] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 10:16:09.240] [jointLog] [info] done
[2023-10-03 10:16:09.399] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 10:16:52.946] [jointLog] [info] Number of decoys : 194
[2023-10-03 10:16:52.946] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 10:16:55.389] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 10:16:56.119] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 10:17:35.838] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-03 10:17:35.842] [jointLog] [info] Thread saw mini-batch with a maximum of 4.71% zero probability fragments
[2023-10-03 10:17:35.889] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 10:17:36.096] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-03 10:17:36.177] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-03 10:17:36.196] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-03 10:17:36.405] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-03 10:17:36.433] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 10:17:36.603] [jointLog] [info] Computed 73,010 rich equivalence classes for further processing
[2023-10-03 10:17:36.603] [jointLog] [info] Counted 1,910,362 total reads in the equivalence classes 
[2023-10-03 10:17:36.604] [fileLog] [info] 
At end of round 0
==================
Observed 2660085 total fragments (2660085 in most recent round)

[2023-10-03 10:17:36.611] [jointLog] [info] Number of mappings discarded because of alignment score : 37,350,317
[2023-10-03 10:17:36.611] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 223,060
[2023-10-03 10:17:36.612] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 73,757
[2023-10-03 10:17:36.612] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 10:17:37.940] [jointLog] [warning] Only 1910362 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 10:17:37.940] [jointLog] [info] Mapping rate = 71.8158%

[2023-10-03 10:17:37.940] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 10:17:37.941] [jointLog] [info] Starting optimizer
[2023-10-03 10:17:42.145] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 10:17:42.484] [jointLog] [info] iteration = 0 | max rel diff. = 37.9894
[2023-10-03 10:17:45.873] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 10:18:39.188] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 10:18:39.189] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 10:18:44.240] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 10:18:49.429] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 10:18:54.913] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 10:19:00.181] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 10:19:05.151] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 10:19:09.838] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 10:19:14.306] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 10:19:18.884] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 10:19:23.504] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 10:19:27.913] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 10:19:58.218] [jointLog] [info] iteration = 100 | max rel diff. = 1.3286
[2023-10-03 10:20:33.198] [jointLog] [info] iteration = 200 | max rel diff. = 2.49393
[2023-10-03 10:21:08.394] [jointLog] [info] iteration = 300 | max rel diff. = 0.268326
[2023-10-03 10:21:43.542] [jointLog] [info] iteration = 400 | max rel diff. = 0.16892
[2023-10-03 10:22:19.907] [jointLog] [info] iteration = 500 | max rel diff. = 0.058744
[2023-10-03 10:22:56.308] [jointLog] [info] iteration = 600 | max rel diff. = 0.0733013
[2023-10-03 10:23:33.086] [jointLog] [info] iteration = 700 | max rel diff. = 0.117462
[2023-10-03 10:24:09.789] [jointLog] [info] iteration = 800 | max rel diff. = 1.48493
[2023-10-03 10:24:10.557] [jointLog] [info] iteration = 803 | max rel diff. = 0.00229831
[2023-10-03 10:24:12.730] [jointLog] [info] Finished optimizer
[2023-10-03 10:24:12.730] [jointLog] [info] writing output