[2023-09-24 09:53:48.146] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 09:53:48.146] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 09:53:48.146] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 09:53:48.146] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 09:53:48.146] [jointLog] [info] parsing read library format
[2023-09-24 09:53:48.146] [jointLog] [info] There is 1 library.
[2023-09-24 09:53:48.146] [jointLog] [info] Loading pufferfish index
[2023-09-24 09:53:48.146] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 09:55:04.221] [jointLog] [info] done
[2023-09-24 09:55:04.341] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 09:55:42.660] [jointLog] [info] Number of decoys : 194
[2023-09-24 09:55:42.660] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 09:55:45.025] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 09:55:45.761] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 09:56:22.249] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-24 09:56:22.299] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-24 09:56:22.339] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-24 09:56:22.350] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-09-24 09:56:22.413] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-24 09:56:22.568] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-24 09:56:22.708] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-24 09:56:22.726] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-24 09:56:22.883] [jointLog] [info] Computed 70,781 rich equivalence classes for further processing
[2023-09-24 09:56:22.883] [jointLog] [info] Counted 2,363,933 total reads in the equivalence classes 
[2023-09-24 09:56:22.892] [jointLog] [info] Number of mappings discarded because of alignment score : 40,471,101
[2023-09-24 09:56:22.892] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 333,780
[2023-09-24 09:56:22.892] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 89,680
[2023-09-24 09:56:22.892] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 09:56:22.884] [fileLog] [info] 
At end of round 0
==================
Observed 3023422 total fragments (3023422 in most recent round)

[2023-09-24 09:56:24.356] [jointLog] [warning] Only 2363933 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 09:56:24.356] [jointLog] [info] Mapping rate = 78.1873%

[2023-09-24 09:56:24.356] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 09:56:24.356] [jointLog] [info] Starting optimizer
[2023-09-24 09:56:28.922] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 09:56:29.266] [jointLog] [info] iteration = 0 | max rel diff. = 77.9176
[2023-09-24 09:56:32.767] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 09:57:17.653] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 09:57:17.653] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 09:57:21.519] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 09:57:25.782] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 09:57:30.293] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 09:57:34.535] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 09:57:38.994] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 09:57:43.295] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 09:57:47.192] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 09:57:51.306] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 09:57:55.459] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 09:57:59.641] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 09:58:30.967] [jointLog] [info] iteration = 100 | max rel diff. = 6.71273
[2023-09-24 09:59:03.638] [jointLog] [info] iteration = 200 | max rel diff. = 0.716993
[2023-09-24 09:59:35.872] [jointLog] [info] iteration = 300 | max rel diff. = 1.37537
[2023-09-24 10:00:08.233] [jointLog] [info] iteration = 400 | max rel diff. = 0.106072
[2023-09-24 10:00:40.803] [jointLog] [info] iteration = 500 | max rel diff. = 0.225632
[2023-09-24 10:01:14.160] [jointLog] [info] iteration = 600 | max rel diff. = 0.105442
[2023-09-24 10:01:45.089] [jointLog] [info] iteration = 695 | max rel diff. = 0.00556452
[2023-09-24 10:01:47.277] [jointLog] [info] Finished optimizer
[2023-09-24 10:01:47.277] [jointLog] [info] writing output