[2023-09-26 14:11:39.437] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 14:11:39.437] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 14:11:39.437] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 14:11:39.437] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 14:11:39.437] [jointLog] [info] parsing read library format
[2023-09-26 14:11:39.437] [jointLog] [info] There is 1 library.
[2023-09-26 14:11:39.437] [jointLog] [info] Loading pufferfish index
[2023-09-26 14:11:39.437] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 14:13:02.906] [jointLog] [info] done
[2023-09-26 14:13:03.063] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 14:13:42.343] [jointLog] [info] Number of decoys : 194
[2023-09-26 14:13:42.343] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 14:13:43.868] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 14:13:44.549] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 14:14:04.703] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-26 14:14:04.846] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-26 14:14:04.852] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-26 14:14:04.870] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-26 14:14:04.972] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-26 14:14:05.009] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-26 14:14:05.095] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-26 14:14:05.114] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-09-26 14:14:05.283] [jointLog] [info] Computed 74,876 rich equivalence classes for further processing
[2023-09-26 14:14:05.283] [jointLog] [info] Counted 1,081,589 total reads in the equivalence classes 
[2023-09-26 14:14:05.290] [jointLog] [warning] 6.67448e-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 17.


[2023-09-26 14:14:05.290] [jointLog] [info] Number of mappings discarded because of alignment score : 22,165,645
[2023-09-26 14:14:05.290] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 147,653
[2023-09-26 14:14:05.290] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 37,159
[2023-09-26 14:14:05.290] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 14:14:05.284] [fileLog] [info] 
At end of round 0
==================
Observed 1498244 total fragments (1498244 in most recent round)

[2023-09-26 14:14:06.288] [jointLog] [warning] Only 1081589 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 14:14:06.288] [jointLog] [info] Mapping rate = 72.1904%

[2023-09-26 14:14:06.288] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 14:14:06.289] [jointLog] [info] Starting optimizer
[2023-09-26 14:14:10.024] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 14:14:10.351] [jointLog] [info] iteration = 0 | max rel diff. = 22.7039
[2023-09-26 14:14:13.757] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 14:15:08.687] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 14:15:08.687] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 14:15:13.502] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 14:15:18.782] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 14:15:23.981] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 14:15:29.147] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 14:15:34.337] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 14:15:39.413] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 14:15:44.640] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 14:15:49.853] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 14:15:55.309] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 14:16:00.396] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 14:16:31.432] [jointLog] [info] iteration = 100 | max rel diff. = 6.16652
[2023-09-26 14:17:05.611] [jointLog] [info] iteration = 200 | max rel diff. = 4.9983
[2023-09-26 14:17:39.377] [jointLog] [info] iteration = 300 | max rel diff. = 0.257837
[2023-09-26 14:18:13.353] [jointLog] [info] iteration = 400 | max rel diff. = 0.0500461
[2023-09-26 14:18:47.469] [jointLog] [info] iteration = 500 | max rel diff. = 0.751522
[2023-09-26 14:19:20.919] [jointLog] [info] iteration = 600 | max rel diff. = 0.608507
[2023-09-26 14:19:42.344] [jointLog] [info] iteration = 664 | max rel diff. = 0.00346221
[2023-09-26 14:19:44.836] [jointLog] [info] Finished optimizer
[2023-09-26 14:19:44.836] [jointLog] [info] writing output