[2022-03-25 01:42:51.441] [jointLog] [info] setting maxHashResizeThreads to 28 [2022-03-25 01:42:51.441] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-03-25 01:42:51.441] [jointLog] [info] numQuantThreads = 22 [2022-03-25 01:42:52.497] [jointLog] [info] replaced 15020 non-ACGT nucleotides with random nucleotides [2022-03-25 01:42:52.690] [fileLog] [info] quantification processed 0 fragments so far [2022-03-25 01:42:53.846] [fileLog] [info] quantification processed 1000000 fragments so far [2022-03-25 01:42:55.043] [fileLog] [info] quantification processed 2000000 fragments so far [2022-03-25 01:42:55.926] [jointLog] [info] The alignment group queue pool has been exhausted. 361051 extra fragments were allocated on the heap to saturate the pool. No new fragments will be allocated [2022-03-25 01:42:56.639] [fileLog] [info] quantification processed 3000000 fragments so far [2022-03-25 01:43:00.481] [fileLog] [info] quantification processed 4000000 fragments so far [2022-03-25 01:43:04.343] [fileLog] [info] quantification processed 5000000 fragments so far [2022-03-25 01:43:08.201] [fileLog] [info] quantification processed 6000000 fragments so far [2022-03-25 01:43:12.067] [fileLog] [info] quantification processed 7000000 fragments so far [2022-03-25 01:43:13.137] [fileLog] [info] quantification processed 8000000 fragments so far [2022-03-25 01:43:14.103] [fileLog] [info] quantification processed 9000000 fragments so far [2022-03-25 01:43:15.247] [fileLog] [info] quantification processed 10000000 fragments so far [2022-03-25 01:43:16.388] [fileLog] [info] quantification processed 11000000 fragments so far [2022-03-25 01:43:17.608] [fileLog] [info] quantification processed 12000000 fragments so far [2022-03-25 01:43:19.049] [fileLog] [info] quantification processed 13000000 fragments so far [2022-03-25 01:43:20.914] [fileLog] [info] quantification processed 14000000 fragments so far [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.90% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 27.60% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 29.70% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 29.10% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.70% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 30.60% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 30.40% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.10% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.60% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 27.90% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 27.20% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 29.80% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.00% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 30.30% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 26.60% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 29.20% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 28.20% zero probability fragments [2022-03-25 01:43:21.482] [jointLog] [info] Thread saw mini-batch with a maximum of 30.50% zero probability fragments [2022-03-25 01:43:21.483] [jointLog] [info] Thread saw mini-batch with a maximum of 28.20% zero probability fragments [2022-03-25 01:43:21.485] [jointLog] [info] Thread saw mini-batch with a maximum of 28.00% zero probability fragments [2022-03-25 01:43:21.487] [jointLog] [info] Thread saw mini-batch with a maximum of 28.30% zero probability fragments [2022-03-25 01:43:21.490] [jointLog] [info] Thread saw mini-batch with a maximum of 28.60% zero probability fragments [2022-03-25 01:43:21.490] [jointLog] [info] Completed first pass through the alignment file. Total # of mapped reads : 14210649 # of uniquely mapped reads : 12276016 # ambiguously mapped reads : 1934633 [2022-03-25 01:43:21.508] [jointLog] [info] Computed 19522 rich equivalence classes for further processing [2022-03-25 01:43:21.508] [jointLog] [info] Counted 11066640 total reads in the equivalence classes [2022-03-25 01:43:21.509] [jointLog] [info] starting optimizer [2022-03-25 01:43:21.524] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2022-03-25 01:43:21.527] [jointLog] [info] iteration = 0 | max rel diff. = 15995.7 [2022-03-25 01:43:21.482] [fileLog] [info] quantification processed 14210649 fragments so far [2022-03-25 01:43:21.746] [jointLog] [info] iteration = 100 | max rel diff. = 16.7419 [2022-03-25 01:43:21.953] [jointLog] [info] iteration = 200 | max rel diff. = 5.2544 [2022-03-25 01:43:22.159] [jointLog] [info] iteration = 300 | max rel diff. = 9.9754 [2022-03-25 01:43:22.366] [jointLog] [info] iteration = 400 | max rel diff. = 0.119217 [2022-03-25 01:43:22.572] [jointLog] [info] iteration = 500 | max rel diff. = 0.257798 [2022-03-25 01:43:22.777] [jointLog] [info] iteration = 600 | max rel diff. = 1.1366 [2022-03-25 01:43:22.981] [jointLog] [info] iteration = 700 | max rel diff. = 0.115394 [2022-03-25 01:43:23.183] [jointLog] [info] iteration = 800 | max rel diff. = 0.463612 [2022-03-25 01:43:23.385] [jointLog] [info] iteration = 900 | max rel diff. = 0.719738 [2022-03-25 01:43:23.588] [jointLog] [info] iteration = 1000 | max rel diff. = 0.062171 [2022-03-25 01:43:23.663] [jointLog] [info] iteration = 1038 | max rel diff. = 0.00417207 [2022-03-25 01:43:23.668] [jointLog] [info] finished optimizer [2022-03-25 01:43:23.668] [jointLog] [info] writing output [2022-03-25 01:43:24.997] [jointLog] [info] Computing gene-level abundance estimates [2022-03-25 01:43:29.450] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes [2022-03-25 01:43:29.450] [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 01:43:29.501] [jointLog] [info] Aggregating expressions to gene level [2022-03-25 01:43:29.579] [jointLog] [info] done