[2023-09-20 23:37:40.686] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 23:37:40.686] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 23:37:40.686] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 23:37:40.686] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 23:37:40.686] [jointLog] [info] parsing read library format
[2023-09-20 23:37:40.686] [jointLog] [info] There is 1 library.
[2023-09-20 23:37:40.686] [jointLog] [info] Loading pufferfish index
[2023-09-20 23:37:40.686] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 23:38:52.871] [jointLog] [info] done
[2023-09-20 23:38:52.999] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 23:39:33.952] [jointLog] [info] Number of decoys : 194
[2023-09-20 23:39:33.952] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 23:39:36.735] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 23:39:37.780] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 23:40:09.259] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
[2023-09-20 23:40:09.319] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-09-20 23:40:09.334] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-20 23:40:09.342] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-09-20 23:40:09.449] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-20 23:40:09.467] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments
[2023-09-20 23:40:09.570] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-20 23:40:09.583] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-20 23:40:09.745] [jointLog] [info] Computed 71,145 rich equivalence classes for further processing
[2023-09-20 23:40:09.745] [jointLog] [info] Counted 1,519,180 total reads in the equivalence classes 
[2023-09-20 23:40:09.753] [jointLog] [info] Number of mappings discarded because of alignment score : 39,534,748
[2023-09-20 23:40:09.753] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 201,006
[2023-09-20 23:40:09.753] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,516
[2023-09-20 23:40:09.753] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 23:40:09.746] [fileLog] [info] 
At end of round 0
==================
Observed 2168107 total fragments (2168107 in most recent round)

[2023-09-20 23:40:11.364] [jointLog] [warning] Only 1519180 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 23:40:11.364] [jointLog] [info] Mapping rate = 70.0694%

[2023-09-20 23:40:11.364] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 23:40:11.365] [jointLog] [info] Starting optimizer
[2023-09-20 23:40:16.446] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 23:40:16.788] [jointLog] [info] iteration = 0 | max rel diff. = 28.9608
[2023-09-20 23:40:20.241] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 23:41:12.859] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 23:41:12.860] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 23:41:17.285] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 23:41:22.196] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 23:41:27.322] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 23:41:32.155] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 23:41:37.129] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 23:41:42.047] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 23:41:46.974] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 23:41:51.686] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 23:41:56.615] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 23:42:01.635] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 23:42:33.883] [jointLog] [info] iteration = 100 | max rel diff. = 1.38989
[2023-09-20 23:43:08.589] [jointLog] [info] iteration = 200 | max rel diff. = 0.592623
[2023-09-20 23:43:43.424] [jointLog] [info] iteration = 300 | max rel diff. = 0.361464
[2023-09-20 23:44:18.209] [jointLog] [info] iteration = 400 | max rel diff. = 0.141854
[2023-09-20 23:44:52.873] [jointLog] [info] iteration = 500 | max rel diff. = 0.35449
[2023-09-20 23:45:27.093] [jointLog] [info] iteration = 600 | max rel diff. = 0.090114
[2023-09-20 23:46:02.246] [jointLog] [info] iteration = 700 | max rel diff. = 0.0616905
[2023-09-20 23:46:26.225] [jointLog] [info] iteration = 770 | max rel diff. = 0.00374859
[2023-09-20 23:46:28.685] [jointLog] [info] Finished optimizer
[2023-09-20 23:46:28.685] [jointLog] [info] writing output