[2023-10-02 12:21:48.781] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 12:21:48.781] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 12:21:48.781] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 12:21:48.781] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 12:21:48.781] [jointLog] [info] parsing read library format
[2023-10-02 12:21:48.781] [jointLog] [info] There is 1 library.
[2023-10-02 12:21:48.781] [jointLog] [info] Loading pufferfish index
[2023-10-02 12:21:48.781] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 12:23:06.395] [jointLog] [info] done
[2023-10-02 12:23:06.525] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 12:23:42.919] [jointLog] [info] Number of decoys : 194
[2023-10-02 12:23:42.919] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 12:23:44.161] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 12:23:45.178] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 12:23:56.494] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 12:23:56.547] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-02 12:23:56.619] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 12:23:56.634] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-02 12:23:56.694] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-02 12:23:56.717] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 12:23:56.728] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-02 12:23:56.783] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-02 12:23:56.887] [jointLog] [info] Computed 50,347 rich equivalence classes for further processing
[2023-10-02 12:23:56.887] [jointLog] [info] Counted 725,223 total reads in the equivalence classes 
[2023-10-02 12:23:56.894] [jointLog] [warning] 0.000106% 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 12:23:56.894] [jointLog] [info] Number of mappings discarded because of alignment score : 10,777,219
[2023-10-02 12:23:56.894] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 61,380
[2023-10-02 12:23:56.894] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 24,002
[2023-10-02 12:23:56.894] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 12:23:56.888] [fileLog] [info] 
At end of round 0
==================
Observed 943398 total fragments (943398 in most recent round)

[2023-10-02 12:23:57.594] [jointLog] [warning] Only 725223 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 12:23:57.594] [jointLog] [info] Mapping rate = 76.8735%

[2023-10-02 12:23:57.594] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 12:23:57.595] [jointLog] [info] Starting optimizer
[2023-10-02 12:24:00.822] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 12:24:01.132] [jointLog] [info] iteration = 0 | max rel diff. = 14.2514
[2023-10-02 12:24:04.322] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 12:24:39.738] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 12:24:39.739] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 12:24:43.114] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 12:24:46.281] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 12:24:49.666] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 12:24:53.006] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 12:24:56.448] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 12:24:59.744] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 12:25:03.064] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 12:25:06.619] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 12:25:09.947] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 12:25:13.230] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 12:25:41.421] [jointLog] [info] iteration = 100 | max rel diff. = 2.05977
[2023-10-02 12:26:13.724] [jointLog] [info] iteration = 200 | max rel diff. = 0.746166
[2023-10-02 12:26:45.859] [jointLog] [info] iteration = 300 | max rel diff. = 0.0321383
[2023-10-02 12:27:17.799] [jointLog] [info] iteration = 400 | max rel diff. = 0.242883
[2023-10-02 12:27:25.595] [jointLog] [info] iteration = 426 | max rel diff. = 0.00972952
[2023-10-02 12:27:27.238] [jointLog] [info] Finished optimizer
[2023-10-02 12:27:27.238] [jointLog] [info] writing output