[2022-03-25 01:00:53.216] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 01:00:53.216] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 01:00:53.216] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-03-25 01:00:53.216] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-03-25 01:00:53.216] [jointLog] [info] parsing read library format
[2022-03-25 01:00:53.217] [jointLog] [info] There is 1 library.
[2022-03-25 01:00:53.294] [jointLog] [info] Loading pufferfish index
[2022-03-25 01:00:53.294] [jointLog] [info] Loading dense pufferfish index.
[2022-03-25 01:01:05.062] [jointLog] [info] done
[2022-03-25 01:01:05.062] [jointLog] [info] Index contained 38052 targets
[2022-03-25 01:01:05.078] [jointLog] [info] Number of decoys : 18
[2022-03-25 01:01:05.078] [jointLog] [info] First decoy index : 38034 
[2022-03-25 01:04:52.962] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-03-25 01:04:52.962] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments
[2022-03-25 01:04:52.962] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments
[2022-03-25 01:04:52.962] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:04:52.964] [jointLog] [info] Thread saw mini-batch with a maximum of 0.94% zero probability fragments
[2022-03-25 01:04:52.964] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:04:52.986] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments
[2022-03-25 01:04:52.998] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:04:53.024] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-03-25 01:04:53.030] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:04:53.041] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-03-25 01:04:53.059] [jointLog] [info] Thread saw mini-batch with a maximum of 0.98% zero probability fragments
[2022-03-25 01:04:53.079] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:04:53.119] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-03-25 01:04:53.133] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-03-25 01:04:53.135] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-03-25 01:04:53.143] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments
[2022-03-25 01:04:53.187] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments
[2022-03-25 01:04:53.192] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-03-25 01:04:53.228] [jointLog] [info] Thread saw mini-batch with a maximum of 1.00% zero probability fragments
[2022-03-25 01:04:53.239] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments
[2022-03-25 01:04:53.248] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-03-25 01:04:53.275] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments
[2022-03-25 01:04:53.281] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments
[2022-03-25 01:04:53.286] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-03-25 01:04:53.292] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-03-25 01:04:53.308] [jointLog] [info] Thread saw mini-batch with a maximum of 0.98% zero probability fragments
[2022-03-25 01:04:53.333] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments
[2022-03-25 01:04:53.513] [jointLog] [info] Computed 29069 rich equivalence classes for further processing
[2022-03-25 01:04:53.513] [jointLog] [info] Counted 10584286 total reads in the equivalence classes 
[2022-03-25 01:04:53.526] [jointLog] [warning] 0.00459324% 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 01:04:53.526] [jointLog] [info] Number of mappings discarded because of alignment score : 7204921
[2022-03-25 01:04:53.526] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4192415
[2022-03-25 01:04:53.526] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 2346818
[2022-03-25 01:04:53.526] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 246568
[2022-03-25 01:04:53.526] [jointLog] [info] Mapping rate = 18.4782%

[2022-03-25 01:04:53.526] [jointLog] [info] finished quantifyLibrary()
[2022-03-25 01:04:53.529] [jointLog] [info] Starting optimizer
[2022-03-25 01:04:53.555] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:04:53.559] [jointLog] [info] iteration = 0 | max rel diff. = 18983.7
[2022-03-25 01:04:53.514] [fileLog] [info] 
At end of round 0
==================
Observed 57279796 total fragments (57279796 in most recent round)

[2022-03-25 01:04:53.825] [jointLog] [info] iteration = 100 | max rel diff. = 2.26716
[2022-03-25 01:04:54.071] [jointLog] [info] iteration = 200 | max rel diff. = 1.71802
[2022-03-25 01:04:54.312] [jointLog] [info] iteration = 300 | max rel diff. = 5.57863
[2022-03-25 01:04:54.523] [jointLog] [info] iteration = 400 | max rel diff. = 0.441375
[2022-03-25 01:04:54.733] [jointLog] [info] iteration = 500 | max rel diff. = 1.93233
[2022-03-25 01:04:54.943] [jointLog] [info] iteration = 600 | max rel diff. = 0.219355
[2022-03-25 01:04:55.134] [jointLog] [info] iteration = 692 | max rel diff. = 0.00606627
[2022-03-25 01:04:55.138] [jointLog] [info] Finished optimizer
[2022-03-25 01:04:55.138] [jointLog] [info] writing output 

[2022-03-25 01:04:55.195] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:04:59.639] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:04:59.639] [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 01:04:59.691] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:04:59.780] [jointLog] [info] done