[2023-10-05 03:13:42.832] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 03:13:42.832] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 03:13:42.832] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 03:13:42.832] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 03:13:42.832] [jointLog] [info] parsing read library format
[2023-10-05 03:13:42.833] [jointLog] [info] There is 1 library.
[2023-10-05 03:13:42.833] [jointLog] [info] Loading pufferfish index
[2023-10-05 03:13:42.833] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 03:14:58.493] [jointLog] [info] done
[2023-10-05 03:14:58.614] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 03:15:35.812] [jointLog] [info] Number of decoys : 194
[2023-10-05 03:15:35.812] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 03:15:37.414] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 03:15:38.441] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 03:16:06.170] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-05 03:16:06.263] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-05 03:16:06.268] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-05 03:16:06.406] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-05 03:16:06.426] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-05 03:16:06.444] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-05 03:16:06.613] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-05 03:16:06.648] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-05 03:16:06.789] [jointLog] [info] Computed 65,685 rich equivalence classes for further processing
[2023-10-05 03:16:06.789] [jointLog] [info] Counted 1,364,375 total reads in the equivalence classes 
[2023-10-05 03:16:06.796] [jointLog] [warning] 5.45647e-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.


[2023-10-05 03:16:06.796] [jointLog] [info] Number of mappings discarded because of alignment score : 31,008,830
[2023-10-05 03:16:06.796] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 172,329
[2023-10-05 03:16:06.796] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 53,932
[2023-10-05 03:16:06.796] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 03:16:06.789] [fileLog] [info] 
At end of round 0
==================
Observed 1832686 total fragments (1832686 in most recent round)

[2023-10-05 03:16:07.767] [jointLog] [warning] Only 1364375 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 03:16:07.767] [jointLog] [info] Mapping rate = 74.4467%

[2023-10-05 03:16:07.767] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 03:16:07.767] [jointLog] [info] Starting optimizer
[2023-10-05 03:16:11.699] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 03:16:12.024] [jointLog] [info] iteration = 0 | max rel diff. = 31.0285
[2023-10-05 03:16:15.310] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 03:17:00.418] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 03:17:00.419] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 03:17:04.161] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 03:17:08.242] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 03:17:12.417] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 03:17:16.597] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 03:17:20.456] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 03:17:24.784] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 03:17:28.705] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 03:17:32.999] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 03:17:36.915] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 03:17:41.199] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 03:18:11.125] [jointLog] [info] iteration = 100 | max rel diff. = 0.643668
[2023-10-05 03:18:42.160] [jointLog] [info] iteration = 200 | max rel diff. = 0.169699
[2023-10-05 03:19:13.024] [jointLog] [info] iteration = 300 | max rel diff. = 0.199908
[2023-10-05 03:19:44.023] [jointLog] [info] iteration = 400 | max rel diff. = 0.0306342
[2023-10-05 03:20:14.882] [jointLog] [info] iteration = 500 | max rel diff. = 0.498592
[2023-10-05 03:20:15.829] [jointLog] [info] iteration = 504 | max rel diff. = 0.00600438
[2023-10-05 03:20:17.751] [jointLog] [info] Finished optimizer
[2023-10-05 03:20:17.751] [jointLog] [info] writing output