[2022-03-25 01:34:53.107] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 01:34:53.107] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 01:34:53.107] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-03-25 01:34:53.107] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-03-25 01:34:53.107] [jointLog] [info] parsing read library format
[2022-03-25 01:34:53.108] [jointLog] [info] There is 1 library.
[2022-03-25 01:34:53.185] [jointLog] [info] Loading pufferfish index
[2022-03-25 01:34:53.185] [jointLog] [info] Loading dense pufferfish index.
[2022-03-25 01:35:04.248] [jointLog] [info] done
[2022-03-25 01:35:04.248] [jointLog] [info] Index contained 38052 targets
[2022-03-25 01:35:04.259] [jointLog] [info] Number of decoys : 18
[2022-03-25 01:35:04.259] [jointLog] [info] First decoy index : 38034 
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.82% zero probability fragments
[2022-03-25 01:39:46.225] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:39:46.226] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-03-25 01:39:46.227] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.228] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-03-25 01:39:46.232] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:39:46.284] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.287] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.304] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.304] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-03-25 01:39:46.315] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:39:46.347] [jointLog] [info] Thread saw mini-batch with a maximum of 0.66% zero probability fragments
[2022-03-25 01:39:46.368] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.389] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.393] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:39:46.440] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.446] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.461] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-03-25 01:39:46.488] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.496] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments
[2022-03-25 01:39:46.504] [jointLog] [info] Thread saw mini-batch with a maximum of 0.70% zero probability fragments
[2022-03-25 01:39:46.518] [jointLog] [info] Thread saw mini-batch with a maximum of 0.68% zero probability fragments
[2022-03-25 01:39:46.526] [jointLog] [info] Thread saw mini-batch with a maximum of 0.78% zero probability fragments
[2022-03-25 01:39:46.547] [jointLog] [info] Thread saw mini-batch with a maximum of 0.72% zero probability fragments
[2022-03-25 01:39:46.730] [jointLog] [info] Computed 30963 rich equivalence classes for further processing
[2022-03-25 01:39:46.730] [jointLog] [info] Counted 15914799 total reads in the equivalence classes 
[2022-03-25 01:39:46.745] [jointLog] [warning] 0.00545981% 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 01:39:46.745] [jointLog] [info] Number of mappings discarded because of alignment score : 10957308
[2022-03-25 01:39:46.745] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 6318771
[2022-03-25 01:39:46.745] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 3305611
[2022-03-25 01:39:46.745] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 213303
[2022-03-25 01:39:46.745] [jointLog] [info] Mapping rate = 22.0874%

[2022-03-25 01:39:46.745] [jointLog] [info] finished quantifyLibrary()
[2022-03-25 01:39:46.747] [jointLog] [info] Starting optimizer
[2022-03-25 01:39:46.772] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:39:46.776] [jointLog] [info] iteration = 0 | max rel diff. = 28040.4
[2022-03-25 01:39:46.731] [fileLog] [info] 
At end of round 0
==================
Observed 72053841 total fragments (72053841 in most recent round)

[2022-03-25 01:39:47.041] [jointLog] [info] iteration = 100 | max rel diff. = 2.69711
[2022-03-25 01:39:47.288] [jointLog] [info] iteration = 200 | max rel diff. = 0.995341
[2022-03-25 01:39:47.529] [jointLog] [info] iteration = 300 | max rel diff. = 17.2414
[2022-03-25 01:39:47.740] [jointLog] [info] iteration = 400 | max rel diff. = 0.312824
[2022-03-25 01:39:47.950] [jointLog] [info] iteration = 500 | max rel diff. = 0.0290961
[2022-03-25 01:39:48.160] [jointLog] [info] iteration = 600 | max rel diff. = 0.390307
[2022-03-25 01:39:48.371] [jointLog] [info] iteration = 700 | max rel diff. = 0.013535
[2022-03-25 01:39:48.581] [jointLog] [info] iteration = 800 | max rel diff. = 2.16611
[2022-03-25 01:39:48.791] [jointLog] [info] iteration = 900 | max rel diff. = 1.68085
[2022-03-25 01:39:49.001] [jointLog] [info] iteration = 1000 | max rel diff. = 0.019521
[2022-03-25 01:39:49.211] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0712461
[2022-03-25 01:39:49.241] [jointLog] [info] iteration = 1115 | max rel diff. = 0.00476104
[2022-03-25 01:39:49.245] [jointLog] [info] Finished optimizer
[2022-03-25 01:39:49.245] [jointLog] [info] writing output 

[2022-03-25 01:39:49.308] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:39:53.735] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:39:53.735] [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 01:39:53.789] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:39:53.869] [jointLog] [info] done