[2023-10-03 15:11:55.999] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 15:11:55.999] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 15:11:55.999] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 15:11:55.999] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 15:11:55.999] [jointLog] [info] parsing read library format
[2023-10-03 15:11:56.000] [jointLog] [info] There is 1 library.
[2023-10-03 15:11:56.000] [jointLog] [info] Loading pufferfish index
[2023-10-03 15:11:56.000] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 15:13:09.695] [jointLog] [info] done
[2023-10-03 15:13:09.855] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 15:13:49.908] [jointLog] [info] Number of decoys : 194
[2023-10-03 15:13:49.908] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 15:13:51.570] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 15:13:52.684] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 15:15:11.173] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-10-03 15:15:11.190] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 15:15:11.207] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-10-03 15:15:11.241] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-03 15:15:11.397] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-03 15:15:11.638] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-03 15:15:11.704] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-03 15:15:11.810] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-10-03 15:15:12.039] [jointLog] [info] Computed 102,464 rich equivalence classes for further processing
[2023-10-03 15:15:12.039] [jointLog] [info] Counted 2,933,323 total reads in the equivalence classes 
[2023-10-03 15:15:12.077] [jointLog] [info] Number of mappings discarded because of alignment score : 106,473,294
[2023-10-03 15:15:12.077] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 386,598
[2023-10-03 15:15:12.077] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 113,932
[2023-10-03 15:15:12.077] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 15:15:12.039] [fileLog] [info] 
At end of round 0
==================
Observed 4285988 total fragments (4285988 in most recent round)

[2023-10-03 15:15:13.320] [jointLog] [warning] Only 2933323 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 15:15:13.320] [jointLog] [info] Mapping rate = 68.4398%

[2023-10-03 15:15:13.320] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 15:15:13.320] [jointLog] [info] Starting optimizer
[2023-10-03 15:15:18.707] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 15:15:19.043] [jointLog] [info] iteration = 0 | max rel diff. = 66.1547
[2023-10-03 15:15:22.415] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 15:16:25.367] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 15:16:25.368] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 15:16:30.987] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 15:16:36.234] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 15:16:42.019] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 15:16:47.538] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 15:16:53.305] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 15:16:59.487] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 15:17:05.223] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 15:17:11.013] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 15:17:16.680] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 15:17:22.377] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 15:17:52.290] [jointLog] [info] iteration = 100 | max rel diff. = 13.6002
[2023-10-03 15:18:25.731] [jointLog] [info] iteration = 200 | max rel diff. = 12.6137
[2023-10-03 15:18:59.193] [jointLog] [info] iteration = 300 | max rel diff. = 2.48959
[2023-10-03 15:19:32.608] [jointLog] [info] iteration = 400 | max rel diff. = 0.313246
[2023-10-03 15:20:06.126] [jointLog] [info] iteration = 500 | max rel diff. = 0.147033
[2023-10-03 15:20:39.414] [jointLog] [info] iteration = 600 | max rel diff. = 0.0211813
[2023-10-03 15:21:12.951] [jointLog] [info] iteration = 700 | max rel diff. = 0.0539675
[2023-10-03 15:21:46.623] [jointLog] [info] iteration = 800 | max rel diff. = 0.036551
[2023-10-03 15:22:20.122] [jointLog] [info] iteration = 900 | max rel diff. = 0.0379502
[2023-10-03 15:22:53.739] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0442194
[2023-10-03 15:23:08.835] [jointLog] [info] iteration = 1,046 | max rel diff. = 0.00273341
[2023-10-03 15:23:11.518] [jointLog] [info] Finished optimizer
[2023-10-03 15:23:11.518] [jointLog] [info] writing output