[2023-08-28 09:20:23.329] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 09:20:23.329] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 09:20:23.329] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 09:20:23.329] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 09:20:23.329] [jointLog] [info] parsing read library format
[2023-08-28 09:20:23.329] [jointLog] [info] There is 1 library.
[2023-08-28 09:20:23.329] [jointLog] [info] Loading pufferfish index
[2023-08-28 09:20:23.329] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 09:21:50.244] [jointLog] [info] done
[2023-08-28 09:21:50.432] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 09:22:32.172] [jointLog] [info] Number of decoys : 194
[2023-08-28 09:22:32.172] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 09:22:34.438] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-28 09:22:35.975] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-28 09:28:14.614] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-08-28 09:28:14.654] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-08-28 09:28:14.951] [jointLog] [info] Thread saw mini-batch with a maximum of 4.60% zero probability fragments
[2023-08-28 09:28:15.057] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-08-28 09:28:15.114] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-08-28 09:28:15.319] [jointLog] [info] Thread saw mini-batch with a maximum of 4.28% zero probability fragments
[2023-08-28 09:28:15.343] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-08-28 09:28:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-08-28 09:28:15.771] [fileLog] [info] 
At end of round 0
==================
Observed 14449015 total fragments (14449015 in most recent round)

[2023-08-28 09:28:15.770] [jointLog] [info] Computed 209,381 rich equivalence classes for further processing
[2023-08-28 09:28:15.770] [jointLog] [info] Counted 6,908,985 total reads in the equivalence classes 
[2023-08-28 09:28:15.778] [jointLog] [info] Number of mappings discarded because of alignment score : 461,464,622
[2023-08-28 09:28:15.778] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,089,169
[2023-08-28 09:28:15.778] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 342,738
[2023-08-28 09:28:15.778] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-28 09:28:15.778] [jointLog] [info] Mapping rate = 47.8163%

[2023-08-28 09:28:15.778] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 09:28:15.779] [jointLog] [info] Starting optimizer
[2023-08-28 09:28:22.346] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 09:28:22.747] [jointLog] [info] iteration = 0 | max rel diff. = 134.184
[2023-08-28 09:28:26.380] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 09:29:47.517] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 09:29:47.518] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 09:29:54.785] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 09:30:02.558] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 09:30:10.089] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 09:30:17.706] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 09:30:25.156] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 09:30:32.445] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 09:30:39.962] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 09:30:47.447] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 09:30:55.062] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 09:31:02.961] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 09:31:34.845] [jointLog] [info] iteration = 100 | max rel diff. = 8.51738
[2023-08-28 09:32:10.207] [jointLog] [info] iteration = 200 | max rel diff. = 0.2831
[2023-08-28 09:32:45.741] [jointLog] [info] iteration = 300 | max rel diff. = 0.730445
[2023-08-28 09:33:18.997] [jointLog] [info] iteration = 400 | max rel diff. = 19.8856
[2023-08-28 09:33:54.398] [jointLog] [info] iteration = 500 | max rel diff. = 2.97715
[2023-08-28 09:34:29.576] [jointLog] [info] iteration = 600 | max rel diff. = 0.097867
[2023-08-28 09:35:04.786] [jointLog] [info] iteration = 700 | max rel diff. = 0.059252
[2023-08-28 09:35:39.971] [jointLog] [info] iteration = 800 | max rel diff. = 0.0477757
[2023-08-28 09:35:47.333] [jointLog] [info] iteration = 822 | max rel diff. = 0.00988563
[2023-08-28 09:35:49.633] [jointLog] [info] Finished optimizer
[2023-08-28 09:35:49.633] [jointLog] [info] writing output