[2023-10-03 20:19:28.096] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 20:19:28.096] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 20:19:28.096] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 20:19:28.096] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 20:19:28.096] [jointLog] [info] parsing read library format
[2023-10-03 20:19:28.097] [jointLog] [info] There is 1 library.
[2023-10-03 20:19:28.097] [jointLog] [info] Loading pufferfish index
[2023-10-03 20:19:28.097] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 20:20:48.208] [jointLog] [info] done
[2023-10-03 20:20:48.368] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 20:21:29.516] [jointLog] [info] Number of decoys : 194
[2023-10-03 20:21:29.516] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 20:21:31.179] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 20:21:31.919] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 20:22:16.583] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-10-03 20:22:16.587] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-03 20:22:16.673] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-10-03 20:22:16.734] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-10-03 20:22:16.748] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-10-03 20:22:16.819] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-03 20:22:16.880] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-10-03 20:22:16.896] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-03 20:22:17.083] [jointLog] [info] Computed 74,459 rich equivalence classes for further processing
[2023-10-03 20:22:17.083] [jointLog] [info] Counted 2,147,583 total reads in the equivalence classes 
[2023-10-03 20:22:17.091] [jointLog] [info] Number of mappings discarded because of alignment score : 49,356,269
[2023-10-03 20:22:17.091] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 271,849
[2023-10-03 20:22:17.091] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 81,280
[2023-10-03 20:22:17.091] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 20:22:17.084] [fileLog] [info] 
At end of round 0
==================
Observed 3718398 total fragments (3718398 in most recent round)

[2023-10-03 20:22:18.256] [jointLog] [warning] Only 2147583 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 20:22:18.256] [jointLog] [info] Mapping rate = 57.7556%

[2023-10-03 20:22:18.256] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 20:22:18.256] [jointLog] [info] Starting optimizer
[2023-10-03 20:22:23.786] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 20:22:24.127] [jointLog] [info] iteration = 0 | max rel diff. = 41.9067
[2023-10-03 20:22:27.483] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 20:23:17.341] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 20:23:17.342] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 20:23:21.694] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 20:23:25.982] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 20:23:30.298] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 20:23:35.074] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 20:23:39.806] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 20:23:44.439] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 20:23:48.991] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 20:23:53.544] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 20:23:57.806] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 20:24:02.354] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 20:24:33.462] [jointLog] [info] iteration = 100 | max rel diff. = 9.43394
[2023-10-03 20:25:07.562] [jointLog] [info] iteration = 200 | max rel diff. = 1.40213
[2023-10-03 20:25:40.958] [jointLog] [info] iteration = 300 | max rel diff. = 2.24045
[2023-10-03 20:26:13.743] [jointLog] [info] iteration = 400 | max rel diff. = 0.339296
[2023-10-03 20:26:45.258] [jointLog] [info] iteration = 500 | max rel diff. = 0.117323
[2023-10-03 20:27:16.378] [jointLog] [info] iteration = 600 | max rel diff. = 0.0320166
[2023-10-03 20:27:48.719] [jointLog] [info] iteration = 700 | max rel diff. = 0.0246772
[2023-10-03 20:28:18.454] [jointLog] [info] iteration = 794 | max rel diff. = 0.00315721
[2023-10-03 20:28:20.534] [jointLog] [info] Finished optimizer
[2023-10-03 20:28:20.534] [jointLog] [info] writing output