[2023-10-05 06:22:06.817] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 06:22:06.817] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 06:22:06.817] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 06:22:06.817] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 06:22:06.817] [jointLog] [info] parsing read library format
[2023-10-05 06:22:06.817] [jointLog] [info] There is 1 library.
[2023-10-05 06:22:06.818] [jointLog] [info] Loading pufferfish index
[2023-10-05 06:22:06.818] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 06:23:23.263] [jointLog] [info] done
[2023-10-05 06:23:23.387] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 06:24:01.054] [jointLog] [info] Number of decoys : 194
[2023-10-05 06:24:01.054] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 06:24:02.781] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 06:24:03.651] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 06:24:27.902] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-10-05 06:24:27.989] [jointLog] [info] Thread saw mini-batch with a maximum of 4.48% zero probability fragments
[2023-10-05 06:24:28.019] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-10-05 06:24:28.064] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-10-05 06:24:28.091] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-10-05 06:24:28.111] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-10-05 06:24:28.142] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-10-05 06:24:28.193] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
[2023-10-05 06:24:28.313] [jointLog] [info] Computed 62,593 rich equivalence classes for further processing
[2023-10-05 06:24:28.313] [jointLog] [info] Counted 1,353,944 total reads in the equivalence classes 
[2023-10-05 06:24:28.319] [jointLog] [info] Number of mappings discarded because of alignment score : 24,658,649
[2023-10-05 06:24:28.319] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 160,773
[2023-10-05 06:24:28.319] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,744
[2023-10-05 06:24:28.319] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 06:24:28.313] [fileLog] [info] 
At end of round 0
==================
Observed 1949331 total fragments (1949331 in most recent round)

[2023-10-05 06:24:29.541] [jointLog] [warning] Only 1353944 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 06:24:29.541] [jointLog] [info] Mapping rate = 69.4569%

[2023-10-05 06:24:29.541] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 06:24:29.541] [jointLog] [info] Starting optimizer
[2023-10-05 06:24:33.914] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 06:24:34.249] [jointLog] [info] iteration = 0 | max rel diff. = 25.489
[2023-10-05 06:24:37.574] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 06:25:25.893] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 06:25:25.893] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 06:25:30.012] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 06:25:34.445] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 06:25:39.040] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 06:25:43.451] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 06:25:48.175] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 06:25:52.707] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 06:25:56.879] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 06:26:01.304] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 06:26:05.717] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 06:26:10.133] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 06:26:40.125] [jointLog] [info] iteration = 100 | max rel diff. = 17.0053
[2023-10-05 06:27:13.626] [jointLog] [info] iteration = 200 | max rel diff. = 8.5724
[2023-10-05 06:27:46.133] [jointLog] [info] iteration = 300 | max rel diff. = 0.22275
[2023-10-05 06:28:18.257] [jointLog] [info] iteration = 400 | max rel diff. = 0.0468404
[2023-10-05 06:28:50.435] [jointLog] [info] iteration = 500 | max rel diff. = 0.022755
[2023-10-05 06:29:22.594] [jointLog] [info] iteration = 600 | max rel diff. = 0.0861559
[2023-10-05 06:29:26.727] [jointLog] [info] iteration = 614 | max rel diff. = 0.00154694
[2023-10-05 06:29:28.440] [jointLog] [info] Finished optimizer
[2023-10-05 06:29:28.440] [jointLog] [info] writing output