[2023-09-16 02:12:41.446] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 02:12:41.446] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 02:12:41.446] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 02:12:41.446] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 02:12:41.446] [jointLog] [info] parsing read library format
[2023-09-16 02:12:41.446] [jointLog] [info] There is 1 library.
[2023-09-16 02:12:41.446] [jointLog] [info] Loading pufferfish index
[2023-09-16 02:12:41.446] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 02:13:54.409] [jointLog] [info] done
[2023-09-16 02:13:54.537] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 02:14:34.485] [jointLog] [info] Number of decoys : 194
[2023-09-16 02:14:34.485] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 02:14:36.454] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 02:14:37.361] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 02:15:20.627] [jointLog] [info] Thread saw mini-batch with a maximum of 10.48% zero probability fragments
[2023-09-16 02:15:20.668] [jointLog] [info] Thread saw mini-batch with a maximum of 9.96% zero probability fragments
[2023-09-16 02:15:20.696] [jointLog] [info] Thread saw mini-batch with a maximum of 10.22% zero probability fragments
[2023-09-16 02:15:20.710] [jointLog] [info] Thread saw mini-batch with a maximum of 10.08% zero probability fragments
[2023-09-16 02:15:20.796] [jointLog] [info] Thread saw mini-batch with a maximum of 9.88% zero probability fragments
[2023-09-16 02:15:20.829] [jointLog] [info] Thread saw mini-batch with a maximum of 9.84% zero probability fragments
[2023-09-16 02:15:20.834] [jointLog] [info] Thread saw mini-batch with a maximum of 9.88% zero probability fragments
[2023-09-16 02:15:20.850] [jointLog] [info] Thread saw mini-batch with a maximum of 9.94% zero probability fragments
[2023-09-16 02:15:21.136] [jointLog] [info] Computed 198,199 rich equivalence classes for further processing
[2023-09-16 02:15:21.136] [jointLog] [info] Counted 4,947,117 total reads in the equivalence classes 
[2023-09-16 02:15:21.145] [jointLog] [info] Number of mappings discarded because of alignment score : 11,851,781
[2023-09-16 02:15:21.145] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 114,281
[2023-09-16 02:15:21.145] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,339
[2023-09-16 02:15:21.145] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 02:15:21.137] [fileLog] [info] 
At end of round 0
==================
Observed 5821615 total fragments (5821615 in most recent round)

[2023-09-16 02:15:22.896] [jointLog] [warning] Only 4947117 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-16 02:15:22.896] [jointLog] [info] Mapping rate = 84.9784%

[2023-09-16 02:15:22.896] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 02:15:22.897] [jointLog] [info] Starting optimizer
[2023-09-16 02:15:27.547] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 02:15:27.898] [jointLog] [info] iteration = 0 | max rel diff. = 132.3
[2023-09-16 02:15:31.418] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 02:16:52.721] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 02:16:52.721] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 02:17:00.066] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 02:17:07.396] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 02:17:14.695] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 02:17:22.427] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 02:17:29.900] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 02:17:36.976] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 02:17:44.213] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 02:17:52.073] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 02:17:59.894] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 02:18:07.276] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 02:18:39.278] [jointLog] [info] iteration = 100 | max rel diff. = 20.2723
[2023-09-16 02:19:15.505] [jointLog] [info] iteration = 200 | max rel diff. = 7.22656
[2023-09-16 02:19:50.395] [jointLog] [info] iteration = 300 | max rel diff. = 3.5629
[2023-09-16 02:20:22.741] [jointLog] [info] iteration = 400 | max rel diff. = 1.43653
[2023-09-16 02:20:54.668] [jointLog] [info] iteration = 500 | max rel diff. = 4.01823
[2023-09-16 02:21:26.881] [jointLog] [info] iteration = 600 | max rel diff. = 0.446795
[2023-09-16 02:21:59.080] [jointLog] [info] iteration = 700 | max rel diff. = 1.66814
[2023-09-16 02:22:30.631] [jointLog] [info] iteration = 800 | max rel diff. = 0.124036
[2023-09-16 02:23:02.171] [jointLog] [info] iteration = 900 | max rel diff. = 0.0404429
[2023-09-16 02:23:34.145] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0488877
[2023-09-16 02:23:41.247] [jointLog] [info] iteration = 1,023 | max rel diff. = 0.0050484
[2023-09-16 02:23:43.400] [jointLog] [info] Finished optimizer
[2023-09-16 02:23:43.400] [jointLog] [info] writing output