[2022-03-25 01:12:29.041] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 01:12:29.041] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 01:12:29.041] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-03-25 01:12:29.041] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-03-25 01:12:29.041] [jointLog] [info] parsing read library format
[2022-03-25 01:12:29.042] [jointLog] [info] There is 1 library.
[2022-03-25 01:12:29.120] [jointLog] [info] Loading pufferfish index
[2022-03-25 01:12:29.120] [jointLog] [info] Loading dense pufferfish index.
[2022-03-25 01:12:40.860] [jointLog] [info] done
[2022-03-25 01:12:40.860] [jointLog] [info] Index contained 38052 targets
[2022-03-25 01:12:40.872] [jointLog] [info] Number of decoys : 18
[2022-03-25 01:12:40.872] [jointLog] [info] First decoy index : 38034 
[2022-03-25 01:34:35.645] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.663] [jointLog] [info] Thread saw mini-batch with a maximum of 0.54% zero probability fragments
[2022-03-25 01:34:35.677] [jointLog] [info] Thread saw mini-batch with a maximum of 0.68% zero probability fragments
[2022-03-25 01:34:35.724] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.728] [jointLog] [info] Thread saw mini-batch with a maximum of 0.62% zero probability fragments
[2022-03-25 01:34:35.780] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.64% zero probability fragments
[2022-03-25 01:34:35.782] [jointLog] [info] Thread saw mini-batch with a maximum of 0.62% zero probability fragments
[2022-03-25 01:34:35.792] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:34:35.798] [jointLog] [info] Thread saw mini-batch with a maximum of 0.54% zero probability fragments
[2022-03-25 01:34:35.839] [jointLog] [info] Thread saw mini-batch with a maximum of 0.56% zero probability fragments
[2022-03-25 01:34:35.855] [jointLog] [info] Thread saw mini-batch with a maximum of 5.36% zero probability fragments
[2022-03-25 01:34:35.871] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2022-03-25 01:34:35.874] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2022-03-25 01:34:35.920] [jointLog] [info] Thread saw mini-batch with a maximum of 0.60% zero probability fragments
[2022-03-25 01:34:35.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.929] [jointLog] [info] Thread saw mini-batch with a maximum of 0.60% zero probability fragments
[2022-03-25 01:34:35.930] [jointLog] [info] Thread saw mini-batch with a maximum of 0.54% zero probability fragments
[2022-03-25 01:34:35.951] [jointLog] [info] Thread saw mini-batch with a maximum of 0.68% zero probability fragments
[2022-03-25 01:34:35.953] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.953] [jointLog] [info] Thread saw mini-batch with a maximum of 0.64% zero probability fragments
[2022-03-25 01:34:35.960] [jointLog] [info] Thread saw mini-batch with a maximum of 0.56% zero probability fragments
[2022-03-25 01:34:35.980] [jointLog] [info] Thread saw mini-batch with a maximum of 0.58% zero probability fragments
[2022-03-25 01:34:35.982] [jointLog] [info] Thread saw mini-batch with a maximum of 0.64% zero probability fragments
[2022-03-25 01:34:35.983] [jointLog] [info] Thread saw mini-batch with a maximum of 5.54% zero probability fragments
[2022-03-25 01:34:35.986] [jointLog] [info] Thread saw mini-batch with a maximum of 0.60% zero probability fragments
[2022-03-25 01:34:36.012] [jointLog] [info] Thread saw mini-batch with a maximum of 0.52% zero probability fragments
[2022-03-25 01:34:36.025] [jointLog] [info] Thread saw mini-batch with a maximum of 0.60% zero probability fragments
[2022-03-25 01:34:36.220] [jointLog] [info] Computed 50903 rich equivalence classes for further processing
[2022-03-25 01:34:36.220] [jointLog] [info] Counted 65852820 total reads in the equivalence classes 
[2022-03-25 01:34:36.234] [jointLog] [warning] 0.00141053% 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 01:34:36.234] [jointLog] [info] Number of mappings discarded because of alignment score : 47536677
[2022-03-25 01:34:36.234] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 27594533
[2022-03-25 01:34:36.234] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 14750615
[2022-03-25 01:34:36.234] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1049679
[2022-03-25 01:34:36.234] [jointLog] [info] Mapping rate = 20.1579%

[2022-03-25 01:34:36.234] [jointLog] [info] finished quantifyLibrary()
[2022-03-25 01:34:36.257] [jointLog] [info] Starting optimizer
[2022-03-25 01:34:36.285] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:34:36.288] [jointLog] [info] iteration = 0 | max rel diff. = 167.579
[2022-03-25 01:34:36.220] [fileLog] [info] 
At end of round 0
==================
Observed 326684823 total fragments (326684823 in most recent round)

[2022-03-25 01:34:36.563] [jointLog] [info] iteration = 100 | max rel diff. = 4.26065
[2022-03-25 01:34:36.818] [jointLog] [info] iteration = 200 | max rel diff. = 6.43859
[2022-03-25 01:34:37.056] [jointLog] [info] iteration = 300 | max rel diff. = 0.136324
[2022-03-25 01:34:37.275] [jointLog] [info] iteration = 400 | max rel diff. = 0.030052
[2022-03-25 01:34:37.494] [jointLog] [info] iteration = 500 | max rel diff. = 0.130284
[2022-03-25 01:34:37.713] [jointLog] [info] iteration = 600 | max rel diff. = 0.0924452
[2022-03-25 01:34:37.931] [jointLog] [info] iteration = 700 | max rel diff. = 0.024737
[2022-03-25 01:34:38.150] [jointLog] [info] iteration = 800 | max rel diff. = 0.04321
[2022-03-25 01:34:38.207] [jointLog] [info] iteration = 827 | max rel diff. = 0.0088621
[2022-03-25 01:34:38.210] [jointLog] [info] Finished optimizer
[2022-03-25 01:34:38.210] [jointLog] [info] writing output 

[2022-03-25 01:34:38.272] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:34:42.690] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:34:42.690] [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 01:34:42.790] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:34:42.890] [jointLog] [info] done