[2023-10-03 11:14:08.396] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 11:14:08.396] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 11:14:08.396] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 11:14:08.396] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 11:14:08.396] [jointLog] [info] parsing read library format
[2023-10-03 11:14:08.396] [jointLog] [info] There is 1 library.
[2023-10-03 11:14:08.397] [jointLog] [info] Loading pufferfish index
[2023-10-03 11:14:08.397] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 11:15:30.821] [jointLog] [info] done
[2023-10-03 11:15:30.950] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 11:16:09.655] [jointLog] [info] Number of decoys : 194
[2023-10-03 11:16:09.655] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 11:16:11.439] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 11:16:12.494] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 11:16:57.333] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-03 11:16:57.417] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 11:16:57.501] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-03 11:16:57.574] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-03 11:16:57.693] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-03 11:16:57.735] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 11:16:57.738] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 11:16:57.813] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-03 11:16:57.996] [jointLog] [info] Computed 71,774 rich equivalence classes for further processing
[2023-10-03 11:16:57.996] [jointLog] [info] Counted 2,169,330 total reads in the equivalence classes 
[2023-10-03 11:16:58.003] [jointLog] [warning] 3.36971e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2023-10-03 11:16:58.003] [jointLog] [info] Number of mappings discarded because of alignment score : 51,696,265
[2023-10-03 11:16:58.003] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 286,448
[2023-10-03 11:16:58.003] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 88,525
[2023-10-03 11:16:58.003] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 11:16:57.996] [fileLog] [info] 
At end of round 0
==================
Observed 2967617 total fragments (2967617 in most recent round)

[2023-10-03 11:16:58.996] [jointLog] [warning] Only 2169330 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 11:16:58.996] [jointLog] [info] Mapping rate = 73.1001%

[2023-10-03 11:16:58.996] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 11:16:58.996] [jointLog] [info] Starting optimizer
[2023-10-03 11:17:03.270] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 11:17:03.624] [jointLog] [info] iteration = 0 | max rel diff. = 49.8459
[2023-10-03 11:17:07.103] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 11:17:56.986] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 11:17:56.987] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 11:18:01.384] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 11:18:05.685] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 11:18:10.386] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 11:18:15.005] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 11:18:19.647] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 11:18:24.409] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 11:18:28.770] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 11:18:33.074] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 11:18:37.089] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 11:18:41.515] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 11:19:10.768] [jointLog] [info] iteration = 100 | max rel diff. = 9.38448
[2023-10-03 11:19:44.094] [jointLog] [info] iteration = 200 | max rel diff. = 9.78664
[2023-10-03 11:20:16.681] [jointLog] [info] iteration = 300 | max rel diff. = 1.97452
[2023-10-03 11:20:49.166] [jointLog] [info] iteration = 400 | max rel diff. = 0.360807
[2023-10-03 11:21:21.482] [jointLog] [info] iteration = 500 | max rel diff. = 0.0196324
[2023-10-03 11:21:54.153] [jointLog] [info] iteration = 600 | max rel diff. = 0.159504
[2023-10-03 11:22:12.885] [jointLog] [info] iteration = 657 | max rel diff. = 0.00836463
[2023-10-03 11:22:14.933] [jointLog] [info] Finished optimizer
[2023-10-03 11:22:14.933] [jointLog] [info] writing output