[2022-03-25 00:56:10.965] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 00:56:10.965] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 00:56:10.965] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-03-25 00:56:10.965] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-03-25 00:56:10.965] [jointLog] [info] parsing read library format
[2022-03-25 00:56:10.966] [jointLog] [info] There is 1 library.
[2022-03-25 00:56:11.043] [jointLog] [info] Loading pufferfish index
[2022-03-25 00:56:11.043] [jointLog] [info] Loading dense pufferfish index.
[2022-03-25 00:56:22.658] [jointLog] [info] done
[2022-03-25 00:56:22.658] [jointLog] [info] Index contained 38052 targets
[2022-03-25 00:56:22.672] [jointLog] [info] Number of decoys : 18
[2022-03-25 00:56:22.672] [jointLog] [info] First decoy index : 38034 
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.70% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.48% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.38% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.46% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.42% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.14% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.58% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.40% zero probability fragments
[2022-03-25 01:00:35.997] [jointLog] [info] Thread saw mini-batch with a maximum of 6.38% zero probability fragments
[2022-03-25 01:00:35.999] [jointLog] [info] Thread saw mini-batch with a maximum of 6.32% zero probability fragments
[2022-03-25 01:00:36.008] [jointLog] [info] Thread saw mini-batch with a maximum of 6.32% zero probability fragments
[2022-03-25 01:00:36.015] [jointLog] [info] Thread saw mini-batch with a maximum of 6.50% zero probability fragments
[2022-03-25 01:00:36.017] [jointLog] [info] Thread saw mini-batch with a maximum of 6.36% zero probability fragments
[2022-03-25 01:00:36.046] [jointLog] [info] Thread saw mini-batch with a maximum of 6.28% zero probability fragments
[2022-03-25 01:00:36.070] [jointLog] [info] Thread saw mini-batch with a maximum of 6.36% zero probability fragments
[2022-03-25 01:00:36.084] [jointLog] [info] Thread saw mini-batch with a maximum of 6.40% zero probability fragments
[2022-03-25 01:00:36.107] [jointLog] [info] Thread saw mini-batch with a maximum of 6.72% zero probability fragments
[2022-03-25 01:00:36.108] [jointLog] [info] Thread saw mini-batch with a maximum of 6.36% zero probability fragments
[2022-03-25 01:00:36.113] [jointLog] [info] Thread saw mini-batch with a maximum of 6.40% zero probability fragments
[2022-03-25 01:00:36.139] [jointLog] [info] Thread saw mini-batch with a maximum of 6.46% zero probability fragments
[2022-03-25 01:00:36.175] [jointLog] [info] Thread saw mini-batch with a maximum of 6.32% zero probability fragments
[2022-03-25 01:00:36.176] [jointLog] [info] Thread saw mini-batch with a maximum of 6.32% zero probability fragments
[2022-03-25 01:00:36.198] [jointLog] [info] Thread saw mini-batch with a maximum of 6.36% zero probability fragments
[2022-03-25 01:00:36.214] [jointLog] [info] Thread saw mini-batch with a maximum of 6.58% zero probability fragments
[2022-03-25 01:00:36.225] [jointLog] [info] Thread saw mini-batch with a maximum of 7.02% zero probability fragments
[2022-03-25 01:00:36.239] [jointLog] [info] Thread saw mini-batch with a maximum of 6.28% zero probability fragments
[2022-03-25 01:00:36.250] [jointLog] [info] Thread saw mini-batch with a maximum of 6.38% zero probability fragments
[2022-03-25 01:00:36.271] [jointLog] [info] Thread saw mini-batch with a maximum of 6.22% zero probability fragments
[2022-03-25 01:00:36.449] [jointLog] [info] Computed 18703 rich equivalence classes for further processing
[2022-03-25 01:00:36.449] [jointLog] [info] Counted 12401693 total reads in the equivalence classes 
[2022-03-25 01:00:36.463] [jointLog] [warning] 0.00754806% 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 01:00:36.463] [jointLog] [info] Number of mappings discarded because of alignment score : 8441778
[2022-03-25 01:00:36.463] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4782551
[2022-03-25 01:00:36.463] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 2465773
[2022-03-25 01:00:36.463] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 303519
[2022-03-25 01:00:36.463] [jointLog] [info] Mapping rate = 18.907%

[2022-03-25 01:00:36.463] [jointLog] [info] finished quantifyLibrary()
[2022-03-25 01:00:36.466] [jointLog] [info] Starting optimizer
[2022-03-25 01:00:36.488] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:00:36.492] [jointLog] [info] iteration = 0 | max rel diff. = 20054.9
[2022-03-25 01:00:36.449] [fileLog] [info] 
At end of round 0
==================
Observed 65592977 total fragments (65592977 in most recent round)

[2022-03-25 01:00:36.748] [jointLog] [info] iteration = 100 | max rel diff. = 17.478
[2022-03-25 01:00:36.985] [jointLog] [info] iteration = 200 | max rel diff. = 6.79218
[2022-03-25 01:00:37.222] [jointLog] [info] iteration = 300 | max rel diff. = 0.323611
[2022-03-25 01:00:37.425] [jointLog] [info] iteration = 400 | max rel diff. = 0.273961
[2022-03-25 01:00:37.627] [jointLog] [info] iteration = 500 | max rel diff. = 0.354068
[2022-03-25 01:00:37.828] [jointLog] [info] iteration = 600 | max rel diff. = 0.0615443
[2022-03-25 01:00:38.030] [jointLog] [info] iteration = 700 | max rel diff. = 0.0240724
[2022-03-25 01:00:38.232] [jointLog] [info] iteration = 800 | max rel diff. = 0.201753
[2022-03-25 01:00:38.433] [jointLog] [info] iteration = 900 | max rel diff. = 0.153142
[2022-03-25 01:00:38.635] [jointLog] [info] iteration = 1000 | max rel diff. = 0.020865
[2022-03-25 01:00:38.736] [jointLog] [info] iteration = 1051 | max rel diff. = 0.00421632
[2022-03-25 01:00:38.738] [jointLog] [info] Finished optimizer
[2022-03-25 01:00:38.738] [jointLog] [info] writing output 

[2022-03-25 01:00:38.795] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:00:43.222] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:00:43.222] [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 01:00:43.273] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:00:43.352] [jointLog] [info] done