[2023-10-05 10:15:45.141] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 10:15:45.141] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 10:15:45.141] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 10:15:45.141] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 10:15:45.141] [jointLog] [info] parsing read library format
[2023-10-05 10:15:45.142] [jointLog] [info] There is 1 library.
[2023-10-05 10:15:45.142] [jointLog] [info] Loading pufferfish index
[2023-10-05 10:15:45.142] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 10:17:03.702] [jointLog] [info] done
[2023-10-05 10:17:03.854] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 10:17:43.794] [jointLog] [info] Number of decoys : 194
[2023-10-05 10:17:43.794] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 10:17:45.940] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 10:17:46.693] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 10:18:16.313] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-05 10:18:16.360] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-05 10:18:16.388] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-10-05 10:18:16.394] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-10-05 10:18:16.592] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-05 10:18:16.718] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-05 10:18:16.731] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-05 10:18:16.761] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-05 10:18:16.943] [jointLog] [info] Computed 70,402 rich equivalence classes for further processing
[2023-10-05 10:18:16.943] [jointLog] [info] Counted 1,604,811 total reads in the equivalence classes 
[2023-10-05 10:18:16.952] [jointLog] [warning] 4.63123e-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 10.


[2023-10-05 10:18:16.952] [jointLog] [info] Number of mappings discarded because of alignment score : 36,033,649
[2023-10-05 10:18:16.952] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 203,252
[2023-10-05 10:18:16.952] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 65,244
[2023-10-05 10:18:16.952] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 10:18:16.944] [fileLog] [info] 
At end of round 0
==================
Observed 2159253 total fragments (2159253 in most recent round)

[2023-10-05 10:18:18.001] [jointLog] [warning] Only 1604811 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 10:18:18.001] [jointLog] [info] Mapping rate = 74.3225%

[2023-10-05 10:18:18.001] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 10:18:18.001] [jointLog] [info] Starting optimizer
[2023-10-05 10:18:22.349] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 10:18:22.684] [jointLog] [info] iteration = 0 | max rel diff. = 30.4336
[2023-10-05 10:18:26.081] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 10:19:11.245] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 10:19:11.245] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 10:19:15.085] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 10:19:19.352] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 10:19:23.868] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 10:19:28.247] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 10:19:32.322] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 10:19:36.667] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 10:19:40.629] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 10:19:44.910] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 10:19:48.992] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 10:19:53.233] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 10:20:22.559] [jointLog] [info] iteration = 100 | max rel diff. = 6.44602
[2023-10-05 10:20:54.668] [jointLog] [info] iteration = 200 | max rel diff. = 0.247317
[2023-10-05 10:21:27.625] [jointLog] [info] iteration = 300 | max rel diff. = 0.139638
[2023-10-05 10:22:00.753] [jointLog] [info] iteration = 400 | max rel diff. = 0.0400729
[2023-10-05 10:22:33.399] [jointLog] [info] iteration = 500 | max rel diff. = 0.0507684
[2023-10-05 10:22:56.771] [jointLog] [info] iteration = 572 | max rel diff. = 0.00297477
[2023-10-05 10:22:58.897] [jointLog] [info] Finished optimizer
[2023-10-05 10:22:58.897] [jointLog] [info] writing output