[2023-10-03 02:24:20.590] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 02:24:20.590] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 02:24:20.590] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 02:24:20.590] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 02:24:20.590] [jointLog] [info] parsing read library format
[2023-10-03 02:24:20.590] [jointLog] [info] There is 1 library.
[2023-10-03 02:24:20.590] [jointLog] [info] Loading pufferfish index
[2023-10-03 02:24:20.590] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 02:25:33.763] [jointLog] [info] done
[2023-10-03 02:25:33.886] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 02:26:12.760] [jointLog] [info] Number of decoys : 194
[2023-10-03 02:26:12.760] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 02:26:14.602] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 02:26:15.733] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 02:26:45.527] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-03 02:26:45.616] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-03 02:26:45.637] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 02:26:45.828] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 02:26:45.865] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-10-03 02:26:45.892] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 02:26:45.931] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 02:26:45.940] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-03 02:26:46.106] [jointLog] [info] Computed 73,398 rich equivalence classes for further processing
[2023-10-03 02:26:46.106] [jointLog] [info] Counted 1,581,072 total reads in the equivalence classes 
[2023-10-03 02:26:46.113] [jointLog] [info] Number of mappings discarded because of alignment score : 37,673,270
[2023-10-03 02:26:46.113] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 221,571
[2023-10-03 02:26:46.113] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 44,265
[2023-10-03 02:26:46.113] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 02:26:46.107] [fileLog] [info] 
At end of round 0
==================
Observed 2118329 total fragments (2118329 in most recent round)

[2023-10-03 02:26:47.050] [jointLog] [warning] Only 1581072 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 02:26:47.050] [jointLog] [info] Mapping rate = 74.6377%

[2023-10-03 02:26:47.050] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 02:26:47.050] [jointLog] [info] Starting optimizer
[2023-10-03 02:26:50.957] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 02:26:51.285] [jointLog] [info] iteration = 0 | max rel diff. = 30.055
[2023-10-03 02:26:54.582] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 02:27:41.413] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 02:27:41.413] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 02:27:45.314] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 02:27:49.829] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 02:27:54.294] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 02:27:58.867] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 02:28:03.437] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 02:28:08.103] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 02:28:12.131] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 02:28:16.351] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 02:28:20.752] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 02:28:24.915] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 02:28:53.161] [jointLog] [info] iteration = 100 | max rel diff. = 4.30893
[2023-10-03 02:29:24.339] [jointLog] [info] iteration = 200 | max rel diff. = 3.34602
[2023-10-03 02:29:55.363] [jointLog] [info] iteration = 300 | max rel diff. = 1.19738
[2023-10-03 02:30:26.392] [jointLog] [info] iteration = 400 | max rel diff. = 0.132315
[2023-10-03 02:30:57.198] [jointLog] [info] iteration = 500 | max rel diff. = 0.966376
[2023-10-03 02:31:11.981] [jointLog] [info] iteration = 549 | max rel diff. = 0.00898153
[2023-10-03 02:31:13.904] [jointLog] [info] Finished optimizer
[2023-10-03 02:31:13.904] [jointLog] [info] writing output