[2023-09-26 19:12:22.908] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 19:12:22.908] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 19:12:22.908] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 19:12:22.908] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 19:12:22.908] [jointLog] [info] parsing read library format
[2023-09-26 19:12:22.908] [jointLog] [info] There is 1 library.
[2023-09-26 19:12:22.908] [jointLog] [info] Loading pufferfish index
[2023-09-26 19:12:22.908] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 19:13:38.086] [jointLog] [info] done
[2023-09-26 19:13:38.206] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 19:14:16.417] [jointLog] [info] Number of decoys : 194
[2023-09-26 19:14:16.417] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 19:14:18.556] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 19:14:19.331] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 19:14:56.117] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-09-26 19:14:56.149] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-26 19:14:56.196] [jointLog] [info] Thread saw mini-batch with a maximum of 2.60% zero probability fragments
[2023-09-26 19:14:56.208] [jointLog] [info] Thread saw mini-batch with a maximum of 2.52% zero probability fragments
[2023-09-26 19:14:56.271] [jointLog] [info] Thread saw mini-batch with a maximum of 2.60% zero probability fragments
[2023-09-26 19:14:56.306] [jointLog] [info] Thread saw mini-batch with a maximum of 2.56% zero probability fragments
[2023-09-26 19:14:56.315] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-09-26 19:14:56.475] [jointLog] [info] Thread saw mini-batch with a maximum of 2.56% zero probability fragments
[2023-09-26 19:14:56.644] [jointLog] [info] Computed 91,848 rich equivalence classes for further processing
[2023-09-26 19:14:56.644] [jointLog] [info] Counted 2,766,905 total reads in the equivalence classes 
[2023-09-26 19:14:56.653] [jointLog] [info] Number of mappings discarded because of alignment score : 34,312,958
[2023-09-26 19:14:56.653] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 216,780
[2023-09-26 19:14:56.653] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 58,790
[2023-09-26 19:14:56.653] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 19:14:56.644] [fileLog] [info] 
At end of round 0
==================
Observed 3491223 total fragments (3491223 in most recent round)

[2023-09-26 19:14:57.669] [jointLog] [warning] Only 2766905 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 19:14:57.669] [jointLog] [info] Mapping rate = 79.2532%

[2023-09-26 19:14:57.669] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 19:14:57.669] [jointLog] [info] Starting optimizer
[2023-09-26 19:15:02.161] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 19:15:02.500] [jointLog] [info] iteration = 0 | max rel diff. = 58.9286
[2023-09-26 19:15:05.838] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 19:15:58.182] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 19:15:58.183] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 19:16:02.771] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 19:16:07.368] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 19:16:12.187] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 19:16:17.039] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 19:16:21.911] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 19:16:26.956] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 19:16:31.556] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 19:16:35.991] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 19:16:40.635] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 19:16:46.114] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 19:17:16.715] [jointLog] [info] iteration = 100 | max rel diff. = 3.17696
[2023-09-26 19:17:50.888] [jointLog] [info] iteration = 200 | max rel diff. = 0.396576
[2023-09-26 19:18:24.963] [jointLog] [info] iteration = 300 | max rel diff. = 0.664852
[2023-09-26 19:18:59.030] [jointLog] [info] iteration = 400 | max rel diff. = 0.638085
[2023-09-26 19:19:33.235] [jointLog] [info] iteration = 500 | max rel diff. = 0.150152
[2023-09-26 19:20:07.544] [jointLog] [info] iteration = 600 | max rel diff. = 6.31314
[2023-09-26 19:20:40.841] [jointLog] [info] iteration = 700 | max rel diff. = 0.0101435
[2023-09-26 19:21:14.426] [jointLog] [info] iteration = 800 | max rel diff. = 0.0144416
[2023-09-26 19:21:48.242] [jointLog] [info] iteration = 900 | max rel diff. = 0.0926978
[2023-09-26 19:21:52.272] [jointLog] [info] iteration = 913 | max rel diff. = 0.00218016
[2023-09-26 19:21:54.329] [jointLog] [info] Finished optimizer
[2023-09-26 19:21:54.329] [jointLog] [info] writing output