[2023-10-02 16:20:33.413] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 16:20:33.413] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 16:20:33.413] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 16:20:33.413] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 16:20:33.413] [jointLog] [info] parsing read library format
[2023-10-02 16:20:33.413] [jointLog] [info] There is 1 library.
[2023-10-02 16:20:33.413] [jointLog] [info] Loading pufferfish index
[2023-10-02 16:20:33.413] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 16:21:56.899] [jointLog] [info] done
[2023-10-02 16:21:57.051] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 16:22:36.503] [jointLog] [info] Number of decoys : 194
[2023-10-02 16:22:36.503] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 16:22:38.852] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 16:22:40.368] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 16:22:56.517] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 16:22:56.528] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-02 16:22:56.774] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-02 16:22:56.778] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-02 16:22:56.879] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 16:22:56.923] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-02 16:22:57.030] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-10-02 16:22:57.122] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-02 16:22:57.318] [jointLog] [info] Computed 57,979 rich equivalence classes for further processing
[2023-10-02 16:22:57.318] [jointLog] [info] Counted 746,747 total reads in the equivalence classes 
[2023-10-02 16:22:57.330] [jointLog] [warning] 9.95464e-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.


[2023-10-02 16:22:57.330] [jointLog] [info] Number of mappings discarded because of alignment score : 10,649,813
[2023-10-02 16:22:57.330] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 54,227
[2023-10-02 16:22:57.330] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 20,237
[2023-10-02 16:22:57.330] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 16:22:57.319] [fileLog] [info] 
At end of round 0
==================
Observed 1004557 total fragments (1004557 in most recent round)

[2023-10-02 16:22:58.748] [jointLog] [warning] Only 746747 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 16:22:58.748] [jointLog] [info] Mapping rate = 74.336%

[2023-10-02 16:22:58.748] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 16:22:58.748] [jointLog] [info] Starting optimizer
[2023-10-02 16:23:03.950] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 16:23:04.311] [jointLog] [info] iteration = 0 | max rel diff. = 13.9756
[2023-10-02 16:23:08.055] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 16:23:56.064] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 16:23:56.065] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 16:24:00.225] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 16:24:04.573] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 16:24:09.394] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 16:24:13.490] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 16:24:18.256] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 16:24:22.417] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 16:24:26.260] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 16:24:30.319] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 16:24:34.378] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 16:24:38.289] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 16:25:08.322] [jointLog] [info] iteration = 100 | max rel diff. = 5.48599
[2023-10-02 16:25:41.432] [jointLog] [info] iteration = 200 | max rel diff. = 0.474851
[2023-10-02 16:26:15.851] [jointLog] [info] iteration = 300 | max rel diff. = 0.164787
[2023-10-02 16:26:43.494] [jointLog] [info] iteration = 379 | max rel diff. = 0.00956538
[2023-10-02 16:26:46.102] [jointLog] [info] Finished optimizer
[2023-10-02 16:26:46.102] [jointLog] [info] writing output