[2023-10-04 03:11:16.070] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 03:11:16.070] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 03:11:16.070] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 03:11:16.070] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 03:11:16.070] [jointLog] [info] parsing read library format
[2023-10-04 03:11:16.070] [jointLog] [info] There is 1 library.
[2023-10-04 03:11:16.070] [jointLog] [info] Loading pufferfish index
[2023-10-04 03:11:16.070] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 03:12:37.287] [jointLog] [info] done
[2023-10-04 03:12:37.440] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 03:13:16.708] [jointLog] [info] Number of decoys : 194
[2023-10-04 03:13:16.708] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 03:13:18.565] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 03:13:19.349] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 03:14:01.930] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-04 03:14:01.938] [jointLog] [info] Thread saw mini-batch with a maximum of 4.85% zero probability fragments
[2023-10-04 03:14:01.948] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-04 03:14:01.977] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-04 03:14:02.068] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-04 03:14:02.117] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 03:14:02.143] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 03:14:02.352] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-04 03:14:02.497] [jointLog] [info] Computed 71,969 rich equivalence classes for further processing
[2023-10-04 03:14:02.497] [jointLog] [info] Counted 2,824,105 total reads in the equivalence classes 
[2023-10-04 03:14:02.505] [jointLog] [info] Number of mappings discarded because of alignment score : 53,505,396
[2023-10-04 03:14:02.505] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 265,927
[2023-10-04 03:14:02.505] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 77,516
[2023-10-04 03:14:02.505] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 03:14:02.498] [fileLog] [info] 
At end of round 0
==================
Observed 3680639 total fragments (3680639 in most recent round)

[2023-10-04 03:14:03.499] [jointLog] [warning] Only 2824105 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 03:14:03.499] [jointLog] [info] Mapping rate = 76.7287%

[2023-10-04 03:14:03.499] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 03:14:03.499] [jointLog] [info] Starting optimizer
[2023-10-04 03:14:08.468] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 03:14:08.799] [jointLog] [info] iteration = 0 | max rel diff. = 53.2615
[2023-10-04 03:14:12.098] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 03:14:59.311] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 03:14:59.311] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 03:15:03.534] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 03:15:08.013] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 03:15:12.375] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 03:15:16.902] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 03:15:21.377] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 03:15:25.464] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 03:15:29.639] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 03:15:34.041] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 03:15:38.412] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 03:15:42.453] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 03:16:15.022] [jointLog] [info] iteration = 100 | max rel diff. = 14.4012
[2023-10-04 03:16:47.999] [jointLog] [info] iteration = 200 | max rel diff. = 1.65305
[2023-10-04 03:17:20.992] [jointLog] [info] iteration = 300 | max rel diff. = 0.115136
[2023-10-04 03:17:54.181] [jointLog] [info] iteration = 400 | max rel diff. = 2.25821
[2023-10-04 03:18:27.251] [jointLog] [info] iteration = 500 | max rel diff. = 0.083304
[2023-10-04 03:19:00.137] [jointLog] [info] iteration = 600 | max rel diff. = 0.0330731
[2023-10-04 03:19:17.242] [jointLog] [info] iteration = 653 | max rel diff. = 0.0093909
[2023-10-04 03:19:19.280] [jointLog] [info] Finished optimizer
[2023-10-04 03:19:19.280] [jointLog] [info] writing output