[2023-09-25 22:11:38.119] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 22:11:38.119] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 22:11:38.119] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 22:11:38.119] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 22:11:38.119] [jointLog] [info] parsing read library format
[2023-09-25 22:11:38.119] [jointLog] [info] There is 1 library.
[2023-09-25 22:11:38.119] [jointLog] [info] Loading pufferfish index
[2023-09-25 22:11:38.119] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 22:12:54.775] [jointLog] [info] done
[2023-09-25 22:12:54.928] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 22:13:34.607] [jointLog] [info] Number of decoys : 194
[2023-09-25 22:13:34.607] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 22:13:36.343] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 22:13:37.120] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 22:14:01.829] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-25 22:14:01.983] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-25 22:14:02.008] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-25 22:14:02.074] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-25 22:14:02.214] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-09-25 22:14:02.260] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-09-25 22:14:02.296] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-09-25 22:14:02.438] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-09-25 22:14:02.584] [jointLog] [info] Computed 56,394 rich equivalence classes for further processing
[2023-09-25 22:14:02.584] [jointLog] [info] Counted 1,104,092 total reads in the equivalence classes 
[2023-09-25 22:14:02.592] [jointLog] [info] Number of mappings discarded because of alignment score : 26,498,416
[2023-09-25 22:14:02.592] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 137,668
[2023-09-25 22:14:02.592] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 41,712
[2023-09-25 22:14:02.592] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 22:14:02.585] [fileLog] [info] 
At end of round 0
==================
Observed 1493753 total fragments (1493753 in most recent round)

[2023-09-25 22:14:03.731] [jointLog] [warning] Only 1104092 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-25 22:14:03.731] [jointLog] [info] Mapping rate = 73.914%

[2023-09-25 22:14:03.731] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 22:14:03.732] [jointLog] [info] Starting optimizer
[2023-09-25 22:14:08.446] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 22:14:08.786] [jointLog] [info] iteration = 0 | max rel diff. = 20.7746
[2023-09-25 22:14:12.295] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 22:14:51.806] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 22:14:51.807] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 22:14:55.359] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 22:14:58.964] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 22:15:02.727] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 22:15:06.554] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 22:15:10.471] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 22:15:13.799] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 22:15:17.280] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 22:15:20.975] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 22:15:24.551] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 22:15:28.227] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 22:15:56.358] [jointLog] [info] iteration = 100 | max rel diff. = 9.77194
[2023-09-25 22:16:28.559] [jointLog] [info] iteration = 200 | max rel diff. = 0.269799
[2023-09-25 22:17:00.776] [jointLog] [info] iteration = 300 | max rel diff. = 0.0669098
[2023-09-25 22:17:32.546] [jointLog] [info] iteration = 400 | max rel diff. = 0.0201218
[2023-09-25 22:18:05.207] [jointLog] [info] iteration = 500 | max rel diff. = 0.0306663
[2023-09-25 22:18:37.906] [jointLog] [info] iteration = 600 | max rel diff. = 0.830435
[2023-09-25 22:18:38.577] [jointLog] [info] iteration = 603 | max rel diff. = 0.00448191
[2023-09-25 22:18:40.810] [jointLog] [info] Finished optimizer
[2023-09-25 22:18:40.810] [jointLog] [info] writing output