[2023-09-21 13:14:42.578] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 13:14:42.578] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 13:14:42.578] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 13:14:42.578] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 13:14:42.578] [jointLog] [info] parsing read library format
[2023-09-21 13:14:42.578] [jointLog] [info] There is 1 library.
[2023-09-21 13:14:42.579] [jointLog] [info] Loading pufferfish index
[2023-09-21 13:14:42.579] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 13:16:03.818] [jointLog] [info] done
[2023-09-21 13:16:03.949] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 13:16:40.469] [jointLog] [info] Number of decoys : 194
[2023-09-21 13:16:40.469] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 13:16:42.015] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 13:16:43.464] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 13:18:02.658] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-21 13:18:02.697] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-21 13:18:02.723] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-21 13:18:03.090] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-09-21 13:18:03.102] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-21 13:18:03.176] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-21 13:18:03.289] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-21 13:18:03.313] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-21 13:18:03.502] [jointLog] [info] Computed 107,685 rich equivalence classes for further processing
[2023-09-21 13:18:03.502] [jointLog] [info] Counted 3,181,619 total reads in the equivalence classes 
[2023-09-21 13:18:03.509] [jointLog] [info] Number of mappings discarded because of alignment score : 119,923,046
[2023-09-21 13:18:03.509] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 552,790
[2023-09-21 13:18:03.509] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 99,266
[2023-09-21 13:18:03.509] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 13:18:03.503] [fileLog] [info] 
At end of round 0
==================
Observed 4629515 total fragments (4629515 in most recent round)

[2023-09-21 13:18:05.062] [jointLog] [warning] Only 3181619 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 13:18:05.062] [jointLog] [info] Mapping rate = 68.7247%

[2023-09-21 13:18:05.062] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 13:18:05.063] [jointLog] [info] Starting optimizer
[2023-09-21 13:19:05.997] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 13:19:06.326] [jointLog] [info] iteration = 0 | max rel diff. = 73.3351
[2023-09-21 13:19:09.714] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 13:20:12.705] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 13:20:12.706] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 13:20:18.221] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 13:20:23.914] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 13:20:30.114] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 13:20:36.063] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 13:20:41.633] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 13:20:47.859] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 13:20:53.438] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 13:20:58.975] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 13:21:05.020] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 13:21:10.672] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 13:21:40.486] [jointLog] [info] iteration = 100 | max rel diff. = 8.33857
[2023-09-21 13:22:12.587] [jointLog] [info] iteration = 200 | max rel diff. = 0.70017
[2023-09-21 13:22:44.062] [jointLog] [info] iteration = 300 | max rel diff. = 0.246023
[2023-09-21 13:23:16.920] [jointLog] [info] iteration = 400 | max rel diff. = 0.0885258
[2023-09-21 13:23:50.341] [jointLog] [info] iteration = 500 | max rel diff. = 0.313656
[2023-09-21 13:24:24.202] [jointLog] [info] iteration = 600 | max rel diff. = 0.0744392
[2023-09-21 13:24:57.706] [jointLog] [info] iteration = 700 | max rel diff. = 0.013566
[2023-09-21 13:25:31.329] [jointLog] [info] iteration = 800 | max rel diff. = 0.158931
[2023-09-21 13:26:04.680] [jointLog] [info] iteration = 900 | max rel diff. = 0.0224658
[2023-09-21 13:26:38.040] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0618922
[2023-09-21 13:26:52.949] [jointLog] [info] iteration = 1,039 | max rel diff. = 0.00262256
[2023-09-21 13:26:55.198] [jointLog] [info] Finished optimizer
[2023-09-21 13:26:55.198] [jointLog] [info] writing output