[2022-03-25 01:46:15.916] [jointLog] [info] setting maxHashResizeThreads to 28
[2022-03-25 01:46:15.916] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-03-25 01:46:15.916] [jointLog] [info] numQuantThreads = 22
[2022-03-25 01:46:17.002] [jointLog] [info] replaced 15020 non-ACGT nucleotides with random nucleotides
[2022-03-25 01:46:17.201] [fileLog] [info] quantification processed 0 fragments so far

[2022-03-25 01:46:18.593] [fileLog] [info] quantification processed 1000000 fragments so far

[2022-03-25 01:46:19.895] [fileLog] [info] quantification processed 2000000 fragments so far

[2022-03-25 01:46:20.815] [jointLog] [info] 

The alignment group queue pool has been exhausted.  505961 extra fragments were allocated on the heap to saturate the pool.  No new fragments will be allocated


[2022-03-25 01:46:22.194] [fileLog] [info] quantification processed 3000000 fragments so far

[2022-03-25 01:46:27.073] [fileLog] [info] quantification processed 4000000 fragments so far

[2022-03-25 01:46:31.945] [fileLog] [info] quantification processed 5000000 fragments so far

[2022-03-25 01:46:36.818] [fileLog] [info] quantification processed 6000000 fragments so far

[2022-03-25 01:46:41.737] [fileLog] [info] quantification processed 7000000 fragments so far

[2022-03-25 01:46:42.833] [fileLog] [info] quantification processed 8000000 fragments so far

[2022-03-25 01:46:43.804] [fileLog] [info] quantification processed 9000000 fragments so far

[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 9.20% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 6.80% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 7.80% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 7.90% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.70% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 5.10% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 6.70% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 7.40% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 10.80% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 8.60% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 6.70% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 9.50% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 9.30% zero probability fragments
[2022-03-25 01:46:44.439] [jointLog] [info] Thread saw mini-batch with a maximum of 6.40% zero probability fragments
[2022-03-25 01:46:44.440] [jointLog] [info] Thread saw mini-batch with a maximum of 9.80% zero probability fragments
[2022-03-25 01:46:44.442] [jointLog] [info] Thread saw mini-batch with a maximum of 5.00% zero probability fragments
[2022-03-25 01:46:44.442] [jointLog] [info] Thread saw mini-batch with a maximum of 5.40% zero probability fragments
[2022-03-25 01:46:44.444] [jointLog] [info] Thread saw mini-batch with a maximum of 6.80% zero probability fragments
[2022-03-25 01:46:44.445] [jointLog] [info] 


Completed first pass through the alignment file.
Total # of mapped reads : 9639696
# of uniquely mapped reads : 7833536
# ambiguously mapped reads : 1806160



[2022-03-25 01:46:44.462] [jointLog] [info] Computed 29097 rich equivalence classes for further processing
[2022-03-25 01:46:44.462] [jointLog] [info] Counted 9383404 total reads in the equivalence classes 
[2022-03-25 01:46:44.463] [jointLog] [info] starting optimizer
[2022-03-25 01:46:44.480] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-03-25 01:46:44.482] [jointLog] [info] iteration = 0 | max rel diff. = 17700.5
[2022-03-25 01:46:44.439] [fileLog] [info] quantification processed 9639696 fragments so far

[2022-03-25 01:46:44.701] [jointLog] [info] iteration = 100 | max rel diff. = 4.9586
[2022-03-25 01:46:44.912] [jointLog] [info] iteration = 200 | max rel diff. = 4.0078
[2022-03-25 01:46:45.122] [jointLog] [info] iteration = 300 | max rel diff. = 0.358114
[2022-03-25 01:46:45.332] [jointLog] [info] iteration = 400 | max rel diff. = 0.123531
[2022-03-25 01:46:45.543] [jointLog] [info] iteration = 500 | max rel diff. = 0.39271
[2022-03-25 01:46:45.753] [jointLog] [info] iteration = 600 | max rel diff. = 0.560763
[2022-03-25 01:46:45.963] [jointLog] [info] iteration = 700 | max rel diff. = 1.87166
[2022-03-25 01:46:45.965] [jointLog] [info] iteration = 702 | max rel diff. = 0.00639598
[2022-03-25 01:46:45.969] [jointLog] [info] finished optimizer
[2022-03-25 01:46:45.969] [jointLog] [info] writing output
[2022-03-25 01:46:47.251] [jointLog] [info] Computing gene-level abundance estimates
[2022-03-25 01:46:52.352] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes
[2022-03-25 01:46:52.352] [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 01:46:52.403] [jointLog] [info] Aggregating expressions to gene level
[2022-03-25 01:46:52.483] [jointLog] [info] done