[2022-03-25 00:55:00.838] [jointLog] [info] setting maxHashResizeThreads to 28 [2022-03-25 00:55:00.838] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-03-25 00:55:00.838] [jointLog] [info] numQuantThreads = 22 [2022-03-25 00:55:01.945] [jointLog] [info] replaced 15020 non-ACGT nucleotides with random nucleotides [2022-03-25 00:55:02.141] [fileLog] [info] quantification processed 0 fragments so far [2022-03-25 00:55:03.508] [fileLog] [info] quantification processed 1000000 fragments so far [2022-03-25 00:55:04.936] [fileLog] [info] quantification processed 2000000 fragments so far [2022-03-25 00:55:06.120] [jointLog] [info] The alignment group queue pool has been exhausted. 882789 extra fragments were allocated on the heap to saturate the pool. No new fragments will be allocated [2022-03-25 00:55:07.287] [fileLog] [info] quantification processed 3000000 fragments so far [2022-03-25 00:55:12.324] [fileLog] [info] quantification processed 4000000 fragments so far [2022-03-25 00:55:17.361] [fileLog] [info] quantification processed 5000000 fragments so far [2022-03-25 00:55:22.410] [fileLog] [info] quantification processed 6000000 fragments so far [2022-03-25 00:55:27.409] [fileLog] [info] quantification processed 7000000 fragments so far [2022-03-25 00:55:28.725] [fileLog] [info] quantification processed 8000000 fragments so far [2022-03-25 00:55:29.987] [fileLog] [info] quantification processed 9000000 fragments so far [2022-03-25 00:55:31.479] [fileLog] [info] quantification processed 10000000 fragments so far [2022-03-25 00:55:33.145] [fileLog] [info] quantification processed 11000000 fragments so far [2022-03-25 00:55:35.721] [fileLog] [info] quantification processed 12000000 fragments so far [2022-03-25 00:55:37.903] [fileLog] [info] quantification processed 13000000 fragments so far [2022-03-25 00:55:39.289] [fileLog] [info] quantification processed 14000000 fragments so far [2022-03-25 00:55:40.534] [fileLog] [info] quantification processed 15000000 fragments so far [2022-03-25 00:55:42.012] [fileLog] [info] quantification processed 16000000 fragments so far [2022-03-25 00:55:43.528] [fileLog] [info] quantification processed 17000000 fragments so far [2022-03-25 00:55:45.160] [fileLog] [info] quantification processed 18000000 fragments so far [2022-03-25 00:55:46.702] [fileLog] [info] quantification processed 19000000 fragments so far [2022-03-25 00:55:48.413] [fileLog] [info] quantification processed 20000000 fragments so far [2022-03-25 00:55:49.980] [fileLog] [info] quantification processed 21000000 fragments so far [2022-03-25 00:55:51.390] [fileLog] [info] quantification processed 22000000 fragments so far [2022-03-25 00:55:52.960] [fileLog] [info] quantification processed 23000000 fragments so far [2022-03-25 00:55:53.182] [fileLog] [info] quantification processed 23130036 fragments so far [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 5.50% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 6.70% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.70% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.10% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 5.00% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.20% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.80% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 8.70% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 6.50% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.70% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 6.10% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 8.60% zero probability fragments [2022-03-25 00:55:53.182] [jointLog] [info] Thread saw mini-batch with a maximum of 7.90% zero probability fragments [2022-03-25 00:55:53.187] [jointLog] [info] Thread saw mini-batch with a maximum of 5.50% zero probability fragments [2022-03-25 00:55:53.195] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments [2022-03-25 00:55:53.195] [jointLog] [info] Completed first pass through the alignment file. Total # of mapped reads : 23130036 # of uniquely mapped reads : 16612334 # ambiguously mapped reads : 6517702 [2022-03-25 00:55:53.215] [jointLog] [info] Computed 30777 rich equivalence classes for further processing [2022-03-25 00:55:53.215] [jointLog] [info] Counted 22683444 total reads in the equivalence classes [2022-03-25 00:55:53.216] [jointLog] [info] starting optimizer [2022-03-25 00:55:53.233] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2022-03-25 00:55:53.236] [jointLog] [info] iteration = 0 | max rel diff. = 31168.8 [2022-03-25 00:55:53.463] [jointLog] [info] iteration = 100 | max rel diff. = 2.00909 [2022-03-25 00:55:53.678] [jointLog] [info] iteration = 200 | max rel diff. = 7.02988 [2022-03-25 00:55:53.893] [jointLog] [info] iteration = 300 | max rel diff. = 2.61158 [2022-03-25 00:55:54.109] [jointLog] [info] iteration = 400 | max rel diff. = 1.11523 [2022-03-25 00:55:54.322] [jointLog] [info] iteration = 500 | max rel diff. = 0.270792 [2022-03-25 00:55:54.534] [jointLog] [info] iteration = 600 | max rel diff. = 0.0195717 [2022-03-25 00:55:54.746] [jointLog] [info] iteration = 700 | max rel diff. = 0.766766 [2022-03-25 00:55:54.958] [jointLog] [info] iteration = 800 | max rel diff. = 0.0625651 [2022-03-25 00:55:55.170] [jointLog] [info] iteration = 900 | max rel diff. = 0.0517177 [2022-03-25 00:55:55.365] [jointLog] [info] iteration = 993 | max rel diff. = 0.00926832 [2022-03-25 00:55:55.370] [jointLog] [info] finished optimizer [2022-03-25 00:55:55.370] [jointLog] [info] writing output [2022-03-25 00:55:56.794] [jointLog] [info] Computing gene-level abundance estimates [2022-03-25 00:56:01.313] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes [2022-03-25 00:56:01.313] [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 00:56:01.366] [jointLog] [info] Aggregating expressions to gene level [2022-03-25 00:56:01.445] [jointLog] [info] done