[2023-09-21 09:17:29.895] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 09:17:29.895] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 09:17:29.895] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 09:17:29.895] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 09:17:29.895] [jointLog] [info] parsing read library format
[2023-09-21 09:17:29.895] [jointLog] [info] There is 1 library.
[2023-09-21 09:17:29.895] [jointLog] [info] Loading pufferfish index
[2023-09-21 09:17:29.895] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 09:18:44.882] [jointLog] [info] done
[2023-09-21 09:18:45.012] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 09:19:21.764] [jointLog] [info] Number of decoys : 194
[2023-09-21 09:19:21.764] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 09:19:23.890] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 09:19:24.747] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 09:20:27.159] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-21 09:20:27.160] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-21 09:20:27.260] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-21 09:20:27.376] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-21 09:20:27.409] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-21 09:20:27.429] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-21 09:20:27.479] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-21 09:20:27.520] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-21 09:20:27.712] [jointLog] [info] Computed 104,461 rich equivalence classes for further processing
[2023-09-21 09:20:27.712] [jointLog] [info] Counted 3,520,966 total reads in the equivalence classes 
[2023-09-21 09:20:27.737] [jointLog] [info] Number of mappings discarded because of alignment score : 71,136,817
[2023-09-21 09:20:27.737] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 310,450
[2023-09-21 09:20:27.737] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 92,259
[2023-09-21 09:20:27.737] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 09:20:27.712] [fileLog] [info] 
At end of round 0
==================
Observed 4921584 total fragments (4921584 in most recent round)

[2023-09-21 09:20:28.781] [jointLog] [warning] Only 3520966 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 09:20:28.781] [jointLog] [info] Mapping rate = 71.5413%

[2023-09-21 09:20:28.781] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 09:20:28.782] [jointLog] [info] Starting optimizer
[2023-09-21 09:20:32.844] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 09:20:33.175] [jointLog] [info] iteration = 0 | max rel diff. = 68.0934
[2023-09-21 09:20:36.609] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 09:21:38.167] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 09:21:38.167] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 09:21:43.828] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 09:21:49.533] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 09:21:55.080] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 09:22:01.108] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 09:22:06.759] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 09:22:12.341] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 09:22:17.916] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 09:22:23.552] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 09:22:29.374] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 09:22:34.639] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 09:23:07.135] [jointLog] [info] iteration = 100 | max rel diff. = 3.43789
[2023-09-21 09:23:42.338] [jointLog] [info] iteration = 200 | max rel diff. = 1.21558
[2023-09-21 09:24:16.667] [jointLog] [info] iteration = 300 | max rel diff. = 0.604838
[2023-09-21 09:24:51.276] [jointLog] [info] iteration = 400 | max rel diff. = 0.0818179
[2023-09-21 09:25:26.492] [jointLog] [info] iteration = 500 | max rel diff. = 1.50799
[2023-09-21 09:26:01.432] [jointLog] [info] iteration = 600 | max rel diff. = 0.0235549
[2023-09-21 09:26:36.171] [jointLog] [info] iteration = 700 | max rel diff. = 0.0293707
[2023-09-21 09:27:10.447] [jointLog] [info] iteration = 800 | max rel diff. = 0.103142
[2023-09-21 09:27:43.968] [jointLog] [info] iteration = 900 | max rel diff. = 0.0753795
[2023-09-21 09:27:48.868] [jointLog] [info] iteration = 916 | max rel diff. = 0.00601242
[2023-09-21 09:27:50.859] [jointLog] [info] Finished optimizer
[2023-09-21 09:27:50.859] [jointLog] [info] writing output