[2023-10-02 19:44:02.659] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 19:44:02.659] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 19:44:02.659] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 19:44:02.659] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 19:44:02.659] [jointLog] [info] parsing read library format
[2023-10-02 19:44:02.659] [jointLog] [info] There is 1 library.
[2023-10-02 19:44:02.659] [jointLog] [info] Loading pufferfish index
[2023-10-02 19:44:02.659] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 19:45:22.907] [jointLog] [info] done
[2023-10-02 19:45:23.029] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 19:46:00.948] [jointLog] [info] Number of decoys : 194
[2023-10-02 19:46:00.949] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 19:46:02.680] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 19:46:04.074] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 19:46:57.297] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-02 19:46:57.414] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-02 19:46:57.419] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-02 19:46:57.447] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-02 19:46:57.595] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-02 19:46:57.698] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-02 19:46:57.813] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-02 19:46:57.829] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-02 19:46:57.995] [jointLog] [info] Computed 90,896 rich equivalence classes for further processing
[2023-10-02 19:46:57.995] [jointLog] [info] Counted 2,467,344 total reads in the equivalence classes 
[2023-10-02 19:46:58.002] [jointLog] [info] Number of mappings discarded because of alignment score : 68,382,037
[2023-10-02 19:46:58.002] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 301,417
[2023-10-02 19:46:58.002] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 74,568
[2023-10-02 19:46:58.002] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 19:46:57.995] [fileLog] [info] 
At end of round 0
==================
Observed 3158270 total fragments (3158270 in most recent round)

[2023-10-02 19:46:59.112] [jointLog] [warning] Only 2467344 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 19:46:59.112] [jointLog] [info] Mapping rate = 78.1233%

[2023-10-02 19:46:59.112] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 19:46:59.112] [jointLog] [info] Starting optimizer
[2023-10-02 19:47:03.982] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 19:47:04.322] [jointLog] [info] iteration = 0 | max rel diff. = 53.7979
[2023-10-02 19:47:07.702] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 19:48:04.145] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 19:48:04.145] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 19:48:08.967] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 19:48:14.113] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 19:48:19.396] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 19:48:24.245] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 19:48:29.307] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 19:48:34.251] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 19:48:39.511] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 19:48:44.774] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 19:48:49.857] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 19:48:54.817] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 19:48:54.817] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 19:49:26.046] [jointLog] [info] iteration = 100 | max rel diff. = 2.94959
[2023-10-02 19:50:01.168] [jointLog] [info] iteration = 200 | max rel diff. = 0.913104
[2023-10-02 19:50:35.338] [jointLog] [info] iteration = 300 | max rel diff. = 0.411509
[2023-10-02 19:51:09.841] [jointLog] [info] iteration = 400 | max rel diff. = 0.123522
[2023-10-02 19:51:44.714] [jointLog] [info] iteration = 500 | max rel diff. = 2.16544
[2023-10-02 19:52:19.528] [jointLog] [info] iteration = 600 | max rel diff. = 0.114958
[2023-10-02 19:52:53.855] [jointLog] [info] iteration = 700 | max rel diff. = 0.0259851
[2023-10-02 19:53:28.822] [jointLog] [info] iteration = 800 | max rel diff. = 0.0321559
[2023-10-02 19:53:39.200] [jointLog] [info] iteration = 831 | max rel diff. = 0.00935621
[2023-10-02 19:53:41.304] [jointLog] [info] Finished optimizer
[2023-10-02 19:53:41.304] [jointLog] [info] writing output