[2023-09-21 19:31:47.069] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 19:31:47.069] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 19:31:47.069] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 19:31:47.069] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 19:31:47.069] [jointLog] [info] parsing read library format
[2023-09-21 19:31:47.069] [jointLog] [info] There is 1 library.
[2023-09-21 19:31:47.069] [jointLog] [info] Loading pufferfish index
[2023-09-21 19:31:47.069] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 19:33:02.088] [jointLog] [info] done
[2023-09-21 19:33:02.213] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 19:33:37.992] [jointLog] [info] Number of decoys : 194
[2023-09-21 19:33:37.992] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 19:33:39.163] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 19:33:40.911] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 19:34:06.261] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-21 19:34:06.601] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-09-21 19:34:06.705] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-21 19:34:06.719] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-21 19:34:06.823] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-21 19:34:06.840] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-21 19:34:06.882] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2023-09-21 19:34:06.921] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-21 19:34:07.064] [jointLog] [info] Computed 61,885 rich equivalence classes for further processing
[2023-09-21 19:34:07.064] [jointLog] [info] Counted 990,777 total reads in the equivalence classes 
[2023-09-21 19:34:07.071] [jointLog] [info] Number of mappings discarded because of alignment score : 34,390,907
[2023-09-21 19:34:07.071] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 157,219
[2023-09-21 19:34:07.071] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 37,400
[2023-09-21 19:34:07.071] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 19:34:07.065] [fileLog] [info] 
At end of round 0
==================
Observed 1348236 total fragments (1348236 in most recent round)

[2023-09-21 19:34:08.021] [jointLog] [warning] Only 990777 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 19:34:08.021] [jointLog] [info] Mapping rate = 73.4869%

[2023-09-21 19:34:08.021] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 19:34:08.021] [jointLog] [info] Starting optimizer
[2023-09-21 19:34:11.876] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 19:34:12.200] [jointLog] [info] iteration = 0 | max rel diff. = 21.675
[2023-09-21 19:34:15.431] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 19:35:00.884] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 19:35:00.885] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 19:35:04.918] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 19:35:08.999] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 19:35:13.048] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 19:35:17.251] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 19:35:21.618] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 19:35:25.917] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 19:35:30.111] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 19:35:34.192] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 19:35:38.073] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 19:35:42.755] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 19:36:11.569] [jointLog] [info] iteration = 100 | max rel diff. = 0.990237
[2023-09-21 19:36:43.754] [jointLog] [info] iteration = 200 | max rel diff. = 0.288426
[2023-09-21 19:37:16.140] [jointLog] [info] iteration = 300 | max rel diff. = 0.135987
[2023-09-21 19:37:49.058] [jointLog] [info] iteration = 400 | max rel diff. = 0.844612
[2023-09-21 19:38:21.471] [jointLog] [info] iteration = 500 | max rel diff. = 0.0202541
[2023-09-21 19:38:53.813] [jointLog] [info] iteration = 600 | max rel diff. = 0.0199475
[2023-09-21 19:39:07.791] [jointLog] [info] iteration = 644 | max rel diff. = 0.00125934
[2023-09-21 19:39:09.702] [jointLog] [info] Finished optimizer
[2023-09-21 19:39:09.702] [jointLog] [info] writing output