[2023-09-21 12:27:32.445] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 12:27:32.445] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 12:27:32.445] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 12:27:32.445] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 12:27:32.445] [jointLog] [info] parsing read library format
[2023-09-21 12:27:32.445] [jointLog] [info] There is 1 library.
[2023-09-21 12:27:32.445] [jointLog] [info] Loading pufferfish index
[2023-09-21 12:27:32.445] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 12:28:50.700] [jointLog] [info] done
[2023-09-21 12:28:50.817] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 12:29:28.848] [jointLog] [info] Number of decoys : 194
[2023-09-21 12:29:28.848] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 12:29:30.712] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 12:29:31.925] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 12:30:15.801] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-21 12:30:15.847] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-21 12:30:15.891] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-21 12:30:15.961] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-21 12:30:16.039] [jointLog] [info] Thread saw mini-batch with a maximum of 4.14% zero probability fragments
[2023-09-21 12:30:16.152] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-21 12:30:16.229] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-21 12:30:16.273] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-21 12:30:16.403] [jointLog] [info] Computed 80,979 rich equivalence classes for further processing
[2023-09-21 12:30:16.403] [jointLog] [info] Counted 2,345,485 total reads in the equivalence classes 
[2023-09-21 12:30:16.411] [jointLog] [info] Number of mappings discarded because of alignment score : 47,765,854
[2023-09-21 12:30:16.411] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 243,557
[2023-09-21 12:30:16.411] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,877
[2023-09-21 12:30:16.411] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 12:30:16.404] [fileLog] [info] 
At end of round 0
==================
Observed 3225203 total fragments (3225203 in most recent round)

[2023-09-21 12:30:17.363] [jointLog] [warning] Only 2345485 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 12:30:17.363] [jointLog] [info] Mapping rate = 72.7236%

[2023-09-21 12:30:17.363] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 12:30:17.364] [jointLog] [info] Starting optimizer
[2023-09-21 12:30:21.101] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 12:30:21.430] [jointLog] [info] iteration = 0 | max rel diff. = 56.7281
[2023-09-21 12:30:24.719] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 12:31:19.812] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 12:31:19.812] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 12:31:24.611] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 12:31:29.515] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 12:31:34.937] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 12:31:40.099] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 12:31:45.353] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 12:31:50.395] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 12:31:55.541] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 12:32:00.810] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 12:32:05.781] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 12:32:11.199] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 12:32:40.339] [jointLog] [info] iteration = 100 | max rel diff. = 6.79394
[2023-09-21 12:33:13.781] [jointLog] [info] iteration = 200 | max rel diff. = 0.421608
[2023-09-21 12:33:46.522] [jointLog] [info] iteration = 300 | max rel diff. = 1.40462
[2023-09-21 12:34:19.152] [jointLog] [info] iteration = 400 | max rel diff. = 0.0662973
[2023-09-21 12:34:51.880] [jointLog] [info] iteration = 500 | max rel diff. = 0.428584
[2023-09-21 12:35:24.503] [jointLog] [info] iteration = 600 | max rel diff. = 0.0416781
[2023-09-21 12:35:56.875] [jointLog] [info] iteration = 700 | max rel diff. = 0.33728
[2023-09-21 12:36:03.982] [jointLog] [info] iteration = 723 | max rel diff. = 0.00900862
[2023-09-21 12:36:05.877] [jointLog] [info] Finished optimizer
[2023-09-21 12:36:05.877] [jointLog] [info] writing output