[2023-10-02 21:13:47.634] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 21:13:47.634] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 21:13:47.634] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 21:13:47.634] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 21:13:47.634] [jointLog] [info] parsing read library format
[2023-10-02 21:13:47.634] [jointLog] [info] There is 1 library.
[2023-10-02 21:13:47.634] [jointLog] [info] Loading pufferfish index
[2023-10-02 21:13:47.634] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 21:15:04.186] [jointLog] [info] done
[2023-10-02 21:15:04.331] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 21:15:40.705] [jointLog] [info] Number of decoys : 194
[2023-10-02 21:15:40.705] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 21:15:42.358] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 21:15:43.450] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 21:16:18.333] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-02 21:16:18.396] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-10-02 21:16:18.509] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-02 21:16:18.530] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-02 21:16:18.550] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-10-02 21:16:18.644] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-02 21:16:18.729] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-02 21:16:18.827] [jointLog] [info] Thread saw mini-batch with a maximum of 2.56% zero probability fragments
[2023-10-02 21:16:18.986] [jointLog] [info] Computed 80,298 rich equivalence classes for further processing
[2023-10-02 21:16:18.986] [jointLog] [info] Counted 2,206,393 total reads in the equivalence classes 
[2023-10-02 21:16:18.993] [jointLog] [info] Number of mappings discarded because of alignment score : 40,812,263
[2023-10-02 21:16:18.993] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 276,392
[2023-10-02 21:16:18.993] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 62,185
[2023-10-02 21:16:18.993] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 21:16:18.987] [fileLog] [info] 
At end of round 0
==================
Observed 2881975 total fragments (2881975 in most recent round)

[2023-10-02 21:16:20.296] [jointLog] [warning] Only 2206393 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 21:16:20.296] [jointLog] [info] Mapping rate = 76.5584%

[2023-10-02 21:16:20.296] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 21:16:20.297] [jointLog] [info] Starting optimizer
[2023-10-02 21:16:24.059] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 21:16:24.392] [jointLog] [info] iteration = 0 | max rel diff. = 49.9791
[2023-10-02 21:16:27.685] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 21:17:14.577] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 21:17:14.577] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 21:17:18.844] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 21:17:23.194] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 21:17:27.533] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 21:17:31.977] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 21:17:36.071] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 21:17:40.376] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 21:17:44.435] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 21:17:48.552] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 21:17:52.743] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 21:17:57.153] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 21:17:57.159] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 21:18:26.227] [jointLog] [info] iteration = 100 | max rel diff. = 1.16226
[2023-10-02 21:18:58.521] [jointLog] [info] iteration = 200 | max rel diff. = 0.809036
[2023-10-02 21:19:30.757] [jointLog] [info] iteration = 300 | max rel diff. = 0.764253
[2023-10-02 21:20:03.340] [jointLog] [info] iteration = 400 | max rel diff. = 0.316422
[2023-10-02 21:20:36.120] [jointLog] [info] iteration = 500 | max rel diff. = 1.86516
[2023-10-02 21:21:08.620] [jointLog] [info] iteration = 600 | max rel diff. = 0.356496
[2023-10-02 21:21:41.142] [jointLog] [info] iteration = 700 | max rel diff. = 0.0203224
[2023-10-02 21:22:13.683] [jointLog] [info] iteration = 800 | max rel diff. = 0.0283102
[2023-10-02 21:22:46.108] [jointLog] [info] iteration = 900 | max rel diff. = 0.0483663
[2023-10-02 21:23:00.364] [jointLog] [info] iteration = 945 | max rel diff. = 0.000564489
[2023-10-02 21:23:02.033] [jointLog] [info] Finished optimizer
[2023-10-02 21:23:02.033] [jointLog] [info] writing output