[2023-10-03 22:18:23.388] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 22:18:23.388] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 22:18:23.388] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 22:18:23.388] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 22:18:23.388] [jointLog] [info] parsing read library format
[2023-10-03 22:18:23.388] [jointLog] [info] There is 1 library.
[2023-10-03 22:18:23.388] [jointLog] [info] Loading pufferfish index
[2023-10-03 22:18:23.388] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 22:19:39.771] [jointLog] [info] done
[2023-10-03 22:19:39.929] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 22:20:19.579] [jointLog] [info] Number of decoys : 194
[2023-10-03 22:20:19.579] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 22:20:21.529] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 22:20:22.140] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 22:21:05.821] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 22:21:05.871] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-03 22:21:05.887] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 22:21:05.925] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 22:21:05.925] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-03 22:21:05.957] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 22:21:06.396] [fileLog] [info] 
At end of round 0
==================
Observed 4295322 total fragments (4295322 in most recent round)

[2023-10-03 22:21:06.171] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-03 22:21:06.171] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-03 22:21:06.395] [jointLog] [info] Computed 81,433 rich equivalence classes for further processing
[2023-10-03 22:21:06.395] [jointLog] [info] Counted 3,302,080 total reads in the equivalence classes 
[2023-10-03 22:21:06.409] [jointLog] [warning] 2.32811e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 17.


[2023-10-03 22:21:06.409] [jointLog] [info] Number of mappings discarded because of alignment score : 47,771,886
[2023-10-03 22:21:06.409] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 322,334
[2023-10-03 22:21:06.409] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 104,340
[2023-10-03 22:21:06.409] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 22:21:07.571] [jointLog] [warning] Only 3302080 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 22:21:07.571] [jointLog] [info] Mapping rate = 76.8762%

[2023-10-03 22:21:07.571] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 22:21:07.571] [jointLog] [info] Starting optimizer
[2023-10-03 22:21:12.545] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 22:21:12.880] [jointLog] [info] iteration = 0 | max rel diff. = 64.1058
[2023-10-03 22:21:16.247] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 22:22:09.163] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 22:22:09.164] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 22:22:13.917] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 22:22:18.914] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 22:22:24.077] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 22:22:29.214] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 22:22:34.053] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 22:22:38.746] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 22:22:43.484] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 22:22:48.612] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 22:22:53.672] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 22:22:58.642] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 22:23:31.085] [jointLog] [info] iteration = 100 | max rel diff. = 5.09586
[2023-10-03 22:24:08.362] [jointLog] [info] iteration = 200 | max rel diff. = 3.27473
[2023-10-03 22:24:45.090] [jointLog] [info] iteration = 300 | max rel diff. = 0.568894
[2023-10-03 22:25:21.121] [jointLog] [info] iteration = 400 | max rel diff. = 2.46402
[2023-10-03 22:25:56.781] [jointLog] [info] iteration = 500 | max rel diff. = 0.183266
[2023-10-03 22:26:31.888] [jointLog] [info] iteration = 600 | max rel diff. = 0.0513943
[2023-10-03 22:27:06.003] [jointLog] [info] iteration = 700 | max rel diff. = 2.25701
[2023-10-03 22:27:39.967] [jointLog] [info] iteration = 800 | max rel diff. = 0.0336996
[2023-10-03 22:28:13.338] [jointLog] [info] iteration = 900 | max rel diff. = 0.175586
[2023-10-03 22:28:46.591] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0720219
[2023-10-03 22:28:51.883] [jointLog] [info] iteration = 1,017 | max rel diff. = 0.00340495
[2023-10-03 22:28:54.329] [jointLog] [info] Finished optimizer
[2023-10-03 22:28:54.329] [jointLog] [info] writing output