[2023-09-26 13:13:27.794] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 13:13:27.794] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 13:13:27.794] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 13:13:27.794] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 13:13:27.794] [jointLog] [info] parsing read library format
[2023-09-26 13:13:27.794] [jointLog] [info] There is 1 library.
[2023-09-26 13:13:27.794] [jointLog] [info] Loading pufferfish index
[2023-09-26 13:13:27.794] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 13:14:44.757] [jointLog] [info] done
[2023-09-26 13:14:44.913] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 13:15:24.798] [jointLog] [info] Number of decoys : 194
[2023-09-26 13:15:24.798] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 13:15:26.791] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 13:15:27.713] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 13:15:55.938] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 13:15:56.025] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-09-26 13:15:56.025] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-26 13:15:56.205] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-26 13:15:56.300] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 13:15:56.446] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-09-26 13:15:56.521] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-26 13:15:56.544] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 13:15:56.729] [jointLog] [info] Computed 82,826 rich equivalence classes for further processing
[2023-09-26 13:15:56.729] [jointLog] [info] Counted 1,481,672 total reads in the equivalence classes 
[2023-09-26 13:15:56.736] [jointLog] [warning] 4.93836e-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 10.


[2023-09-26 13:15:56.736] [jointLog] [info] Number of mappings discarded because of alignment score : 28,894,791
[2023-09-26 13:15:56.736] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 215,079
[2023-09-26 13:15:56.736] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 52,057
[2023-09-26 13:15:56.736] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 13:15:56.729] [fileLog] [info] 
At end of round 0
==================
Observed 2024965 total fragments (2024965 in most recent round)

[2023-09-26 13:15:58.125] [jointLog] [warning] Only 1481672 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 13:15:58.125] [jointLog] [info] Mapping rate = 73.1703%

[2023-09-26 13:15:58.125] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 13:15:58.209] [jointLog] [info] Starting optimizer
[2023-09-26 13:16:02.260] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 13:16:02.596] [jointLog] [info] iteration = 0 | max rel diff. = 29.5648
[2023-09-26 13:16:05.963] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 13:17:00.411] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 13:17:00.412] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 13:17:05.284] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 13:17:10.365] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 13:17:15.121] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 13:17:20.016] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 13:17:25.247] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 13:17:29.885] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 13:17:34.945] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 13:17:40.117] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 13:17:45.405] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 13:17:50.569] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 13:18:20.039] [jointLog] [info] iteration = 100 | max rel diff. = 1.70883
[2023-09-26 13:18:52.498] [jointLog] [info] iteration = 200 | max rel diff. = 0.962425
[2023-09-26 13:19:25.178] [jointLog] [info] iteration = 300 | max rel diff. = 0.0852352
[2023-09-26 13:19:57.867] [jointLog] [info] iteration = 400 | max rel diff. = 0.58304
[2023-09-26 13:20:30.982] [jointLog] [info] iteration = 500 | max rel diff. = 0.13046
[2023-09-26 13:21:03.582] [jointLog] [info] iteration = 600 | max rel diff. = 0.182969
[2023-09-26 13:21:05.868] [jointLog] [info] iteration = 608 | max rel diff. = 0.00777804
[2023-09-26 13:21:07.767] [jointLog] [info] Finished optimizer
[2023-09-26 13:21:07.767] [jointLog] [info] writing output