[2023-10-02 23:10:44.663] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 23:10:44.663] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 23:10:44.663] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 23:10:44.663] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 23:10:44.663] [jointLog] [info] parsing read library format
[2023-10-02 23:10:44.663] [jointLog] [info] There is 1 library.
[2023-10-02 23:10:44.663] [jointLog] [info] Loading pufferfish index
[2023-10-02 23:10:44.663] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 23:12:00.693] [jointLog] [info] done
[2023-10-02 23:12:00.835] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 23:12:41.289] [jointLog] [info] Number of decoys : 194
[2023-10-02 23:12:41.289] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 23:12:43.029] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 23:12:43.695] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 23:13:20.276] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-02 23:13:20.317] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-02 23:13:20.326] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-02 23:13:20.355] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-02 23:13:20.459] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-02 23:13:20.474] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-02 23:13:20.506] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-02 23:13:20.560] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-02 23:13:20.780] [jointLog] [info] Computed 97,928 rich equivalence classes for further processing
[2023-10-02 23:13:20.780] [jointLog] [info] Counted 2,560,069 total reads in the equivalence classes 
[2023-10-02 23:13:20.790] [jointLog] [warning] 0.000122202% 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 23:13:20.790] [jointLog] [info] Number of mappings discarded because of alignment score : 30,447,319
[2023-10-02 23:13:20.790] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 182,902
[2023-10-02 23:13:20.790] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 66,980
[2023-10-02 23:13:20.790] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 23:13:20.781] [fileLog] [info] 
At end of round 0
==================
Observed 3273258 total fragments (3273258 in most recent round)

[2023-10-02 23:13:22.030] [jointLog] [warning] Only 2560069 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 23:13:22.030] [jointLog] [info] Mapping rate = 78.2116%

[2023-10-02 23:13:22.030] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 23:13:22.031] [jointLog] [info] Starting optimizer
[2023-10-02 23:13:27.073] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 23:13:27.398] [jointLog] [info] iteration = 0 | max rel diff. = 66.6155
[2023-10-02 23:13:30.697] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 23:14:29.271] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 23:14:29.272] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 23:14:34.307] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 23:14:39.240] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 23:14:44.554] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 23:14:49.877] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 23:14:54.958] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 23:15:00.776] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 23:15:06.024] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 23:15:11.669] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 23:15:17.074] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 23:15:22.177] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 23:15:52.757] [jointLog] [info] iteration = 100 | max rel diff. = 4.68617
[2023-10-02 23:16:25.515] [jointLog] [info] iteration = 200 | max rel diff. = 1.42064
[2023-10-02 23:16:58.216] [jointLog] [info] iteration = 300 | max rel diff. = 18.0754
[2023-10-02 23:17:31.055] [jointLog] [info] iteration = 400 | max rel diff. = 0.234316
[2023-10-02 23:18:04.051] [jointLog] [info] iteration = 500 | max rel diff. = 0.442515
[2023-10-02 23:18:36.969] [jointLog] [info] iteration = 600 | max rel diff. = 0.0230976
[2023-10-02 23:19:09.848] [jointLog] [info] iteration = 700 | max rel diff. = 0.0283205
[2023-10-02 23:19:32.762] [jointLog] [info] iteration = 774 | max rel diff. = 0.00672866
[2023-10-02 23:19:34.612] [jointLog] [info] Finished optimizer
[2023-10-02 23:19:34.612] [jointLog] [info] writing output