[2023-10-02 13:36:03.555] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 13:36:03.555] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 13:36:03.555] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 13:36:03.555] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 13:36:03.555] [jointLog] [info] parsing read library format
[2023-10-02 13:36:03.555] [jointLog] [info] There is 1 library.
[2023-10-02 13:36:03.555] [jointLog] [info] Loading pufferfish index
[2023-10-02 13:36:03.555] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 13:37:21.052] [jointLog] [info] done
[2023-10-02 13:37:21.175] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 13:37:56.639] [jointLog] [info] Number of decoys : 194
[2023-10-02 13:37:56.639] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 13:37:58.222] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 13:37:58.863] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 13:38:15.721] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-10-02 13:38:15.743] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-02 13:38:15.819] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-10-02 13:38:15.846] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-10-02 13:38:15.851] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-10-02 13:38:15.897] [jointLog] [info] Thread saw mini-batch with a maximum of 2.66% zero probability fragments
[2023-10-02 13:38:15.935] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-02 13:38:15.950] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-10-02 13:38:16.069] [jointLog] [info] Computed 60,756 rich equivalence classes for further processing
[2023-10-02 13:38:16.069] [jointLog] [info] Counted 1,288,295 total reads in the equivalence classes 
[2023-10-02 13:38:16.075] [jointLog] [warning] 0.000365192% 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.


[2023-10-02 13:38:16.075] [jointLog] [info] Number of mappings discarded because of alignment score : 14,993,484
[2023-10-02 13:38:16.075] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 99,206
[2023-10-02 13:38:16.075] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 36,801
[2023-10-02 13:38:16.075] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 13:38:16.069] [fileLog] [info] 
At end of round 0
==================
Observed 1642972 total fragments (1642972 in most recent round)

[2023-10-02 13:38:16.980] [jointLog] [warning] Only 1288295 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-02 13:38:16.980] [jointLog] [info] Mapping rate = 78.4125%

[2023-10-02 13:38:16.980] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 13:38:16.980] [jointLog] [info] Starting optimizer
[2023-10-02 13:38:20.656] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 13:38:20.989] [jointLog] [info] iteration = 0 | max rel diff. = 24.035
[2023-10-02 13:38:24.380] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 13:39:06.331] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 13:39:06.331] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 13:39:10.172] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 13:39:14.008] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 13:39:17.950] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 13:39:21.563] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 13:39:25.334] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 13:39:28.881] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 13:39:32.301] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 13:39:36.523] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 13:39:40.277] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 13:39:44.272] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 13:40:14.798] [jointLog] [info] iteration = 100 | max rel diff. = 3.58323
[2023-10-02 13:40:48.070] [jointLog] [info] iteration = 200 | max rel diff. = 0.100076
[2023-10-02 13:41:21.742] [jointLog] [info] iteration = 300 | max rel diff. = 0.0794579
[2023-10-02 13:41:55.153] [jointLog] [info] iteration = 400 | max rel diff. = 0.0588888
[2023-10-02 13:42:27.725] [jointLog] [info] iteration = 500 | max rel diff. = 0.0173593
[2023-10-02 13:42:46.947] [jointLog] [info] iteration = 560 | max rel diff. = 0.0091478
[2023-10-02 13:42:48.643] [jointLog] [info] Finished optimizer
[2023-10-02 13:42:48.643] [jointLog] [info] writing output