[2023-10-04 12:11:27.601] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 12:11:27.601] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 12:11:27.601] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 12:11:27.601] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 12:11:27.601] [jointLog] [info] parsing read library format
[2023-10-04 12:11:27.601] [jointLog] [info] There is 1 library.
[2023-10-04 12:11:27.601] [jointLog] [info] Loading pufferfish index
[2023-10-04 12:11:27.602] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 12:12:39.462] [jointLog] [info] done
[2023-10-04 12:12:39.583] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 12:13:16.399] [jointLog] [info] Number of decoys : 194
[2023-10-04 12:13:16.399] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 12:13:17.510] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 12:13:18.491] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 12:14:00.170] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 12:14:00.196] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-10-04 12:14:00.293] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 12:14:00.341] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-04 12:14:00.362] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-10-04 12:14:00.406] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-10-04 12:14:00.541] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 12:14:00.541] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 12:14:00.703] [jointLog] [info] Computed 75,762 rich equivalence classes for further processing
[2023-10-04 12:14:00.703] [jointLog] [info] Counted 3,108,229 total reads in the equivalence classes 
[2023-10-04 12:14:00.712] [jointLog] [info] Number of mappings discarded because of alignment score : 46,842,525
[2023-10-04 12:14:00.712] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 301,517
[2023-10-04 12:14:00.712] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 91,467
[2023-10-04 12:14:00.712] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 12:14:00.704] [fileLog] [info] 
At end of round 0
==================
Observed 4032419 total fragments (4032419 in most recent round)

[2023-10-04 12:14:01.574] [jointLog] [warning] Only 3108229 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 12:14:01.574] [jointLog] [info] Mapping rate = 77.081%

[2023-10-04 12:14:01.574] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 12:14:01.574] [jointLog] [info] Starting optimizer
[2023-10-04 12:14:05.271] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 12:14:05.602] [jointLog] [info] iteration = 0 | max rel diff. = 74.8165
[2023-10-04 12:14:08.892] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 12:15:01.328] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 12:15:01.328] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 12:15:06.467] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 12:15:11.067] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 12:15:15.901] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 12:15:20.747] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 12:15:25.364] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 12:15:30.116] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 12:15:34.831] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 12:15:39.802] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 12:15:44.277] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 12:15:48.864] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 12:16:16.957] [jointLog] [info] iteration = 100 | max rel diff. = 20.5525
[2023-10-04 12:16:48.198] [jointLog] [info] iteration = 200 | max rel diff. = 1.50506
[2023-10-04 12:17:19.882] [jointLog] [info] iteration = 300 | max rel diff. = 0.756403
[2023-10-04 12:17:52.120] [jointLog] [info] iteration = 400 | max rel diff. = 5.61718
[2023-10-04 12:18:24.103] [jointLog] [info] iteration = 500 | max rel diff. = 6.33687
[2023-10-04 12:18:56.295] [jointLog] [info] iteration = 600 | max rel diff. = 0.0591064
[2023-10-04 12:19:31.189] [jointLog] [info] iteration = 700 | max rel diff. = 0.0196278
[2023-10-04 12:20:06.812] [jointLog] [info] iteration = 800 | max rel diff. = 0.0167798
[2023-10-04 12:20:42.536] [jointLog] [info] iteration = 900 | max rel diff. = 0.0185748
[2023-10-04 12:21:17.789] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0211685
[2023-10-04 12:21:37.107] [jointLog] [info] iteration = 1,055 | max rel diff. = 0.000268593
[2023-10-04 12:21:38.981] [jointLog] [info] Finished optimizer
[2023-10-04 12:21:38.981] [jointLog] [info] writing output