[2023-09-24 19:26:11.231] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 19:26:11.231] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 19:26:11.231] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 19:26:11.231] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 19:26:11.231] [jointLog] [info] parsing read library format
[2023-09-24 19:26:11.231] [jointLog] [info] There is 1 library.
[2023-09-24 19:26:11.231] [jointLog] [info] Loading pufferfish index
[2023-09-24 19:26:11.231] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 19:27:22.376] [jointLog] [info] done
[2023-09-24 19:27:22.490] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 19:28:01.332] [jointLog] [info] Number of decoys : 194
[2023-09-24 19:28:01.332] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 19:28:03.192] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 19:28:04.003] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 19:28:40.638] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-24 19:28:40.876] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-24 19:28:40.887] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-24 19:28:40.892] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-24 19:28:40.921] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-24 19:28:41.135] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-24 19:28:41.169] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-24 19:28:41.281] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-24 19:28:41.417] [jointLog] [info] Computed 70,243 rich equivalence classes for further processing
[2023-09-24 19:28:41.417] [jointLog] [info] Counted 1,898,178 total reads in the equivalence classes 
[2023-09-24 19:28:41.424] [jointLog] [info] Number of mappings discarded because of alignment score : 51,333,257
[2023-09-24 19:28:41.424] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 275,635
[2023-09-24 19:28:41.424] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 82,849
[2023-09-24 19:28:41.424] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 19:28:41.418] [fileLog] [info] 
At end of round 0
==================
Observed 2597748 total fragments (2597748 in most recent round)

[2023-09-24 19:28:42.753] [jointLog] [warning] Only 1898178 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 19:28:42.753] [jointLog] [info] Mapping rate = 73.0701%

[2023-09-24 19:28:42.753] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 19:28:42.753] [jointLog] [info] Starting optimizer
[2023-09-24 19:28:47.642] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 19:28:47.961] [jointLog] [info] iteration = 0 | max rel diff. = 38.9349
[2023-09-24 19:28:51.205] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 19:29:38.937] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 19:29:38.938] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 19:29:43.480] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 19:29:47.589] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 19:29:51.914] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 19:29:56.291] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 19:30:00.872] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 19:30:05.565] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 19:30:09.918] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 19:30:14.508] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 19:30:18.715] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 19:30:23.100] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 19:30:53.669] [jointLog] [info] iteration = 100 | max rel diff. = 2.76161
[2023-09-24 19:31:26.134] [jointLog] [info] iteration = 200 | max rel diff. = 5.05354
[2023-09-24 19:31:58.193] [jointLog] [info] iteration = 300 | max rel diff. = 0.152165
[2023-09-24 19:32:30.228] [jointLog] [info] iteration = 400 | max rel diff. = 0.0466808
[2023-09-24 19:33:02.204] [jointLog] [info] iteration = 500 | max rel diff. = 0.0117539
[2023-09-24 19:33:34.137] [jointLog] [info] iteration = 600 | max rel diff. = 0.432383
[2023-09-24 19:34:06.491] [jointLog] [info] iteration = 700 | max rel diff. = 0.107226
[2023-09-24 19:34:38.882] [jointLog] [info] iteration = 800 | max rel diff. = 0.0634483
[2023-09-24 19:35:11.605] [jointLog] [info] iteration = 900 | max rel diff. = 0.0134765
[2023-09-24 19:35:44.026] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.811287
[2023-09-24 19:35:45.988] [jointLog] [info] iteration = 1,007 | max rel diff. = 0.00452741
[2023-09-24 19:35:47.971] [jointLog] [info] Finished optimizer
[2023-09-24 19:35:47.971] [jointLog] [info] writing output