[2023-09-24 13:16:55.143] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 13:16:55.143] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 13:16:55.143] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 13:16:55.143] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 13:16:55.143] [jointLog] [info] parsing read library format
[2023-09-24 13:16:55.143] [jointLog] [info] There is 1 library.
[2023-09-24 13:16:55.143] [jointLog] [info] Loading pufferfish index
[2023-09-24 13:16:55.143] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 13:18:14.196] [jointLog] [info] done
[2023-09-24 13:18:14.355] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 13:19:02.190] [jointLog] [info] Number of decoys : 194
[2023-09-24 13:19:02.190] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 13:19:04.148] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 13:19:05.253] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 13:19:43.405] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-09-24 13:19:43.426] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-24 13:19:43.449] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-09-24 13:19:43.533] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-24 13:19:43.780] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-24 13:19:43.901] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-09-24 13:19:43.959] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-24 13:19:43.972] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-09-24 13:19:44.114] [jointLog] [info] Computed 61,641 rich equivalence classes for further processing
[2023-09-24 13:19:44.114] [jointLog] [info] Counted 2,081,971 total reads in the equivalence classes 
[2023-09-24 13:19:44.121] [jointLog] [info] Number of mappings discarded because of alignment score : 52,041,978
[2023-09-24 13:19:44.121] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 333,783
[2023-09-24 13:19:44.121] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 75,851
[2023-09-24 13:19:44.121] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 13:19:44.115] [fileLog] [info] 
At end of round 0
==================
Observed 2734423 total fragments (2734423 in most recent round)

[2023-09-24 13:19:45.158] [jointLog] [warning] Only 2081971 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 13:19:45.158] [jointLog] [info] Mapping rate = 76.1393%

[2023-09-24 13:19:45.158] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 13:19:45.158] [jointLog] [info] Starting optimizer
[2023-09-24 13:19:48.863] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 13:19:49.185] [jointLog] [info] iteration = 0 | max rel diff. = 47.4149
[2023-09-24 13:19:52.460] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 13:20:31.430] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 13:20:31.430] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 13:20:35.102] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 13:20:38.670] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 13:20:42.174] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 13:20:46.130] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 13:20:49.792] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 13:20:53.319] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 13:20:57.004] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 13:21:00.526] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 13:21:04.237] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 13:21:08.275] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 13:21:38.401] [jointLog] [info] iteration = 100 | max rel diff. = 7.06434
[2023-09-24 13:22:12.836] [jointLog] [info] iteration = 200 | max rel diff. = 1.57936
[2023-09-24 13:22:47.517] [jointLog] [info] iteration = 300 | max rel diff. = 0.363172
[2023-09-24 13:23:20.874] [jointLog] [info] iteration = 400 | max rel diff. = 0.0341744
[2023-09-24 13:23:56.561] [jointLog] [info] iteration = 500 | max rel diff. = 0.267832
[2023-09-24 13:24:32.024] [jointLog] [info] iteration = 600 | max rel diff. = 0.912357
[2023-09-24 13:25:04.277] [jointLog] [info] iteration = 700 | max rel diff. = 0.194969
[2023-09-24 13:25:06.205] [jointLog] [info] iteration = 707 | max rel diff. = 0.00581873
[2023-09-24 13:25:08.280] [jointLog] [info] Finished optimizer
[2023-09-24 13:25:08.280] [jointLog] [info] writing output