[2023-10-03 06:04:53.493] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 06:04:53.493] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 06:04:53.493] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 06:04:53.493] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 06:04:53.493] [jointLog] [info] parsing read library format
[2023-10-03 06:04:53.493] [jointLog] [info] There is 1 library.
[2023-10-03 06:04:53.493] [jointLog] [info] Loading pufferfish index
[2023-10-03 06:04:53.493] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 06:06:10.482] [jointLog] [info] done
[2023-10-03 06:06:10.628] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 06:06:49.985] [jointLog] [info] Number of decoys : 194
[2023-10-03 06:06:49.985] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 06:06:51.697] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 06:06:52.873] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 06:07:39.532] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 06:07:39.618] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-03 06:07:39.637] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 06:07:39.638] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-03 06:07:39.754] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 06:07:39.809] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 06:07:39.845] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 06:07:39.920] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 06:07:40.058] [jointLog] [info] Computed 95,287 rich equivalence classes for further processing
[2023-10-03 06:07:40.058] [jointLog] [info] Counted 2,409,642 total reads in the equivalence classes 
[2023-10-03 06:07:40.064] [jointLog] [info] Number of mappings discarded because of alignment score : 54,170,164
[2023-10-03 06:07:40.064] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 318,827
[2023-10-03 06:07:40.064] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 73,984
[2023-10-03 06:07:40.064] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 06:07:40.059] [fileLog] [info] 
At end of round 0
==================
Observed 3197759 total fragments (3197759 in most recent round)

[2023-10-03 06:07:41.063] [jointLog] [warning] Only 2409642 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 06:07:41.063] [jointLog] [info] Mapping rate = 75.3541%

[2023-10-03 06:07:41.063] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 06:07:41.063] [jointLog] [info] Starting optimizer
[2023-10-03 06:07:45.565] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 06:07:45.901] [jointLog] [info] iteration = 0 | max rel diff. = 45.7993
[2023-10-03 06:07:49.263] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 06:08:48.858] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 06:08:48.858] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 06:08:54.425] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 06:08:59.921] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 06:09:05.456] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 06:09:11.039] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 06:09:16.567] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 06:09:21.629] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 06:09:26.955] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 06:09:32.053] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 06:09:37.789] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 06:09:42.965] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 06:10:14.190] [jointLog] [info] iteration = 100 | max rel diff. = 15.6819
[2023-10-03 06:10:48.880] [jointLog] [info] iteration = 200 | max rel diff. = 0.78998
[2023-10-03 06:11:23.725] [jointLog] [info] iteration = 300 | max rel diff. = 0.194434
[2023-10-03 06:11:57.562] [jointLog] [info] iteration = 400 | max rel diff. = 0.282882
[2023-10-03 06:12:30.903] [jointLog] [info] iteration = 500 | max rel diff. = 0.322862
[2023-10-03 06:13:04.322] [jointLog] [info] iteration = 600 | max rel diff. = 0.0138516
[2023-10-03 06:13:38.011] [jointLog] [info] iteration = 700 | max rel diff. = 0.022422
[2023-10-03 06:14:11.417] [jointLog] [info] iteration = 800 | max rel diff. = 0.0891332
[2023-10-03 06:14:40.452] [jointLog] [info] iteration = 889 | max rel diff. = 0.00121285
[2023-10-03 06:14:42.327] [jointLog] [info] Finished optimizer
[2023-10-03 06:14:42.327] [jointLog] [info] writing output