[2023-10-03 22:10:11.115] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 22:10:11.115] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 22:10:11.115] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 22:10:11.115] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 22:10:11.115] [jointLog] [info] parsing read library format
[2023-10-03 22:10:11.115] [jointLog] [info] There is 1 library.
[2023-10-03 22:10:11.115] [jointLog] [info] Loading pufferfish index
[2023-10-03 22:10:11.115] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 22:11:28.942] [jointLog] [info] done
[2023-10-03 22:11:29.094] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 22:12:08.461] [jointLog] [info] Number of decoys : 194
[2023-10-03 22:12:08.461] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 22:12:10.315] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 22:12:11.462] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 22:12:49.834] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-03 22:12:49.878] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-03 22:12:49.937] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-03 22:12:50.242] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-03 22:12:50.257] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-10-03 22:12:50.282] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-03 22:12:50.292] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-10-03 22:12:50.300] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-10-03 22:12:50.474] [jointLog] [info] Computed 70,104 rich equivalence classes for further processing
[2023-10-03 22:12:50.474] [jointLog] [info] Counted 2,441,632 total reads in the equivalence classes 
[2023-10-03 22:12:50.481] [jointLog] [info] Number of mappings discarded because of alignment score : 45,309,185
[2023-10-03 22:12:50.481] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 287,046
[2023-10-03 22:12:50.481] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 85,937
[2023-10-03 22:12:50.481] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 22:12:50.475] [fileLog] [info] 
At end of round 0
==================
Observed 3229856 total fragments (3229856 in most recent round)

[2023-10-03 22:12:51.725] [jointLog] [warning] Only 2441632 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 22:12:51.725] [jointLog] [info] Mapping rate = 75.5957%

[2023-10-03 22:12:51.725] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 22:12:51.726] [jointLog] [info] Starting optimizer
[2023-10-03 22:12:56.000] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 22:12:56.334] [jointLog] [info] iteration = 0 | max rel diff. = 52.2408
[2023-10-03 22:12:59.615] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 22:13:46.854] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 22:13:46.855] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 22:13:51.093] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 22:13:55.526] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 22:14:00.253] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 22:14:04.878] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 22:14:09.296] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 22:14:13.654] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 22:14:17.664] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 22:14:22.037] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 22:14:26.129] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 22:14:30.794] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 22:14:59.662] [jointLog] [info] iteration = 100 | max rel diff. = 12.603
[2023-10-03 22:15:31.495] [jointLog] [info] iteration = 200 | max rel diff. = 16.3492
[2023-10-03 22:16:03.293] [jointLog] [info] iteration = 300 | max rel diff. = 1.30044
[2023-10-03 22:16:35.339] [jointLog] [info] iteration = 400 | max rel diff. = 2.76683
[2023-10-03 22:17:07.456] [jointLog] [info] iteration = 500 | max rel diff. = 0.108662
[2023-10-03 22:17:40.378] [jointLog] [info] iteration = 600 | max rel diff. = 0.306755
[2023-10-03 22:17:46.955] [jointLog] [info] iteration = 621 | max rel diff. = 0.00889734
[2023-10-03 22:17:49.056] [jointLog] [info] Finished optimizer
[2023-10-03 22:17:49.056] [jointLog] [info] writing output