[2022-03-25 01:05:10.067] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 01:05:10.067] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 01:05:10.067] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-03-25 01:05:10.067] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-03-25 01:05:10.067] [jointLog] [info] parsing read library format
[2022-03-25 01:05:10.068] [jointLog] [info] There is 1 library.
[2022-03-25 01:05:10.145] [jointLog] [info] Loading pufferfish index
[2022-03-25 01:05:10.145] [jointLog] [info] Loading dense pufferfish index.
[2022-03-25 01:05:21.870] [jointLog] [info] done
[2022-03-25 01:05:21.870] [jointLog] [info] Index contained 38052 targets
[2022-03-25 01:05:21.883] [jointLog] [info] Number of decoys : 18
[2022-03-25 01:05:21.883] [jointLog] [info] First decoy index : 38034 
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 1.08% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.82% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:11.950] [jointLog] [info] Thread saw mini-batch with a maximum of 0.82% zero probability fragments
[2022-03-25 01:12:11.954] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:12:11.958] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-03-25 01:12:12.001] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:12:12.013] [jointLog] [info] Thread saw mini-batch with a maximum of 0.82% zero probability fragments
[2022-03-25 01:12:12.026] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:12:12.042] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:12.050] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:12.070] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:12:12.092] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-03-25 01:12:12.105] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:12.128] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:12:12.141] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:12:12.153] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:12:12.165] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:12:12.348] [jointLog] [info] Computed 32360 rich equivalence classes for further processing
[2022-03-25 01:12:12.348] [jointLog] [info] Counted 25701582 total reads in the equivalence classes 
[2022-03-25 01:12:12.364] [jointLog] [warning] 0.00119618% 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 20.


[2022-03-25 01:12:12.364] [jointLog] [info] Number of mappings discarded because of alignment score : 13918152
[2022-03-25 01:12:12.364] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8587454
[2022-03-25 01:12:12.364] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 4649762
[2022-03-25 01:12:12.364] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 689577
[2022-03-25 01:12:12.364] [jointLog] [info] Mapping rate = 24.7334%

[2022-03-25 01:12:12.364] [jointLog] [info] finished quantifyLibrary()
[2022-03-25 01:12:12.367] [jointLog] [info] Starting optimizer
[2022-03-25 01:12:12.393] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:12:12.397] [jointLog] [info] iteration = 0 | max rel diff. = 32765
[2022-03-25 01:12:12.349] [fileLog] [info] 
At end of round 0
==================
Observed 103914432 total fragments (103914432 in most recent round)

[2022-03-25 01:12:12.671] [jointLog] [info] iteration = 100 | max rel diff. = 1.88907
[2022-03-25 01:12:12.925] [jointLog] [info] iteration = 200 | max rel diff. = 0.257687
[2022-03-25 01:12:13.172] [jointLog] [info] iteration = 300 | max rel diff. = 0.767942
[2022-03-25 01:12:13.388] [jointLog] [info] iteration = 400 | max rel diff. = 0.114535
[2022-03-25 01:12:13.604] [jointLog] [info] iteration = 500 | max rel diff. = 0.0872533
[2022-03-25 01:12:13.820] [jointLog] [info] iteration = 600 | max rel diff. = 0.0180932
[2022-03-25 01:12:14.035] [jointLog] [info] iteration = 700 | max rel diff. = 0.105919
[2022-03-25 01:12:14.251] [jointLog] [info] iteration = 800 | max rel diff. = 0.0745028
[2022-03-25 01:12:14.388] [jointLog] [info] iteration = 865 | max rel diff. = 0.00537374
[2022-03-25 01:12:14.394] [jointLog] [info] Finished optimizer
[2022-03-25 01:12:14.394] [jointLog] [info] writing output 

[2022-03-25 01:12:14.454] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:12:18.864] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:12:18.864] [jointLog] [info] NOTE: We recommend using tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) for aggregating transcript-level salmon abundance estimates to the gene level.  It is more versatile, exposes more features, and allows considering multi-sample information during aggregation.
[2022-03-25 01:12:18.978] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:12:19.109] [jointLog] [info] done