[2023-09-20 06:12:27.806] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 06:12:27.806] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 06:12:27.806] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 06:12:27.806] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 06:12:27.806] [jointLog] [info] parsing read library format
[2023-09-20 06:12:27.807] [jointLog] [info] There is 1 library.
[2023-09-20 06:12:27.807] [jointLog] [info] Loading pufferfish index
[2023-09-20 06:12:27.807] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 06:13:47.211] [jointLog] [info] done
[2023-09-20 06:13:47.388] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 06:14:28.273] [jointLog] [info] Number of decoys : 194
[2023-09-20 06:14:28.273] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 06:14:31.185] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 06:14:32.249] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 06:15:00.460] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-20 06:15:00.475] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-20 06:15:00.489] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-20 06:15:00.496] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-20 06:15:00.622] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-20 06:15:00.713] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-20 06:15:00.760] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-20 06:15:00.838] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-20 06:15:01.054] [fileLog] [info] 
At end of round 0
==================
Observed 2088422 total fragments (2088422 in most recent round)

[2023-09-20 06:15:01.052] [jointLog] [info] Computed 72,966 rich equivalence classes for further processing
[2023-09-20 06:15:01.052] [jointLog] [info] Counted 1,605,092 total reads in the equivalence classes 
[2023-09-20 06:15:01.061] [jointLog] [info] Number of mappings discarded because of alignment score : 32,669,957
[2023-09-20 06:15:01.061] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 168,226
[2023-09-20 06:15:01.061] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 49,157
[2023-09-20 06:15:01.061] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 06:15:02.695] [jointLog] [warning] Only 1605092 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 06:15:02.695] [jointLog] [info] Mapping rate = 76.8567%

[2023-09-20 06:15:02.695] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 06:15:02.696] [jointLog] [info] Starting optimizer
[2023-09-20 06:15:08.885] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 06:15:09.247] [jointLog] [info] iteration = 0 | max rel diff. = 30.4757
[2023-09-20 06:15:12.861] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 06:16:02.579] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 06:16:02.579] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 06:16:07.087] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 06:16:11.503] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 06:16:16.042] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 06:16:20.569] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 06:16:25.297] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 06:16:30.044] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 06:16:34.743] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 06:16:39.080] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 06:16:43.775] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 06:16:48.876] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 06:17:20.955] [jointLog] [info] iteration = 100 | max rel diff. = 4.74576
[2023-09-20 06:17:56.410] [jointLog] [info] iteration = 200 | max rel diff. = 0.670802
[2023-09-20 06:18:31.955] [jointLog] [info] iteration = 300 | max rel diff. = 0.207045
[2023-09-20 06:19:07.334] [jointLog] [info] iteration = 400 | max rel diff. = 0.133953
[2023-09-20 06:19:42.831] [jointLog] [info] iteration = 500 | max rel diff. = 0.180474
[2023-09-20 06:20:17.823] [jointLog] [info] iteration = 600 | max rel diff. = 1.09965
[2023-09-20 06:20:53.204] [jointLog] [info] iteration = 700 | max rel diff. = 0.0971906
[2023-09-20 06:21:28.617] [jointLog] [info] iteration = 800 | max rel diff. = 0.0212363
[2023-09-20 06:21:52.910] [jointLog] [info] iteration = 870 | max rel diff. = 0.00615866
[2023-09-20 06:21:55.021] [jointLog] [info] Finished optimizer
[2023-09-20 06:21:55.021] [jointLog] [info] writing output