[2022-03-25 02:15:01.828] [jointLog] [info] setting maxHashResizeThreads to 28 [2022-03-25 02:15:01.828] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-03-25 02:15:01.828] [jointLog] [info] numQuantThreads = 22 [2022-03-25 02:15:02.827] [jointLog] [info] replaced 15020 non-ACGT nucleotides with random nucleotides [2022-03-25 02:15:03.052] [fileLog] [info] quantification processed 0 fragments so far [2022-03-25 02:15:04.349] [fileLog] [info] quantification processed 1000000 fragments so far [2022-03-25 02:15:05.829] [fileLog] [info] quantification processed 2000000 fragments so far [2022-03-25 02:15:07.004] [jointLog] [info] The alignment group queue pool has been exhausted. 526182 extra fragments were allocated on the heap to saturate the pool. No new fragments will be allocated [2022-03-25 02:15:08.066] [fileLog] [info] quantification processed 3000000 fragments so far [2022-03-25 02:15:13.023] [fileLog] [info] quantification processed 4000000 fragments so far [2022-03-25 02:15:17.938] [fileLog] [info] quantification processed 5000000 fragments so far [2022-03-25 02:15:22.870] [fileLog] [info] quantification processed 6000000 fragments so far [2022-03-25 02:15:27.782] [fileLog] [info] quantification processed 7000000 fragments so far [2022-03-25 02:15:28.919] [fileLog] [info] quantification processed 8000000 fragments so far [2022-03-25 02:15:29.922] [fileLog] [info] quantification processed 9000000 fragments so far [2022-03-25 02:15:30.996] [fileLog] [info] quantification processed 10000000 fragments so far [2022-03-25 02:15:32.066] [fileLog] [info] quantification processed 11000000 fragments so far [2022-03-25 02:15:33.307] [fileLog] [info] quantification processed 12000000 fragments so far [2022-03-25 02:15:34.863] [fileLog] [info] quantification processed 13000000 fragments so far [2022-03-25 02:15:36.534] [fileLog] [info] quantification processed 14000000 fragments so far [2022-03-25 02:15:38.392] [fileLog] [info] quantification processed 15000000 fragments so far [2022-03-25 02:15:40.460] [fileLog] [info] quantification processed 16000000 fragments so far [2022-03-25 02:15:41.941] [fileLog] [info] quantification processed 17000000 fragments so far [2022-03-25 02:15:43.218] [fileLog] [info] quantification processed 18000000 fragments so far [2022-03-25 02:15:44.640] [fileLog] [info] quantification processed 19000000 fragments so far [2022-03-25 02:15:46.163] [fileLog] [info] quantification processed 20000000 fragments so far [2022-03-25 02:15:47.196] [fileLog] [info] quantification processed 21000000 fragments so far [2022-03-25 02:15:48.213] [fileLog] [info] quantification processed 22000000 fragments so far [2022-03-25 02:15:49.303] [fileLog] [info] quantification processed 23000000 fragments so far [2022-03-25 02:15:50.481] [fileLog] [info] quantification processed 24000000 fragments so far [2022-03-25 02:15:51.814] [fileLog] [info] quantification processed 25000000 fragments so far [2022-03-25 02:15:53.285] [fileLog] [info] quantification processed 26000000 fragments so far [2022-03-25 02:15:54.742] [fileLog] [info] quantification processed 27000000 fragments so far [2022-03-25 02:15:56.161] [fileLog] [info] quantification processed 28000000 fragments so far [2022-03-25 02:15:57.500] [fileLog] [info] quantification processed 29000000 fragments so far [2022-03-25 02:15:58.866] [fileLog] [info] quantification processed 30000000 fragments so far [2022-03-25 02:16:00.172] [fileLog] [info] quantification processed 31000000 fragments so far [2022-03-25 02:16:01.494] [fileLog] [info] quantification processed 32000000 fragments so far [2022-03-25 02:16:02.709] [fileLog] [info] quantification processed 33000000 fragments so far [2022-03-25 02:16:04.021] [fileLog] [info] quantification processed 34000000 fragments so far [2022-03-25 02:16:05.429] [fileLog] [info] quantification processed 35000000 fragments so far [2022-03-25 02:16:06.803] [fileLog] [info] quantification processed 36000000 fragments so far [2022-03-25 02:16:08.158] [fileLog] [info] quantification processed 37000000 fragments so far [2022-03-25 02:16:09.524] [fileLog] [info] quantification processed 38000000 fragments so far [2022-03-25 02:16:10.872] [fileLog] [info] quantification processed 39000000 fragments so far [2022-03-25 02:16:12.221] [fileLog] [info] quantification processed 40000000 fragments so far [2022-03-25 02:16:13.684] [fileLog] [info] quantification processed 41000000 fragments so far [2022-03-25 02:16:15.049] [fileLog] [info] quantification processed 42000000 fragments so far [2022-03-25 02:16:16.416] [fileLog] [info] quantification processed 43000000 fragments so far [2022-03-25 02:16:17.840] [fileLog] [info] quantification processed 44000000 fragments so far [2022-03-25 02:16:19.230] [fileLog] [info] quantification processed 45000000 fragments so far [2022-03-25 02:16:20.650] [fileLog] [info] quantification processed 46000000 fragments so far [2022-03-25 02:16:22.321] [fileLog] [info] quantification processed 47000000 fragments so far [2022-03-25 02:16:23.847] [fileLog] [info] quantification processed 48000000 fragments so far [2022-03-25 02:16:25.304] [fileLog] [info] quantification processed 49000000 fragments so far [2022-03-25 02:16:26.703] [fileLog] [info] quantification processed 50000000 fragments so far [2022-03-25 02:16:28.072] [fileLog] [info] quantification processed 51000000 fragments so far [2022-03-25 02:16:29.582] [fileLog] [info] quantification processed 52000000 fragments so far [2022-03-25 02:16:30.996] [fileLog] [info] quantification processed 53000000 fragments so far [2022-03-25 02:16:32.436] [fileLog] [info] quantification processed 54000000 fragments so far [2022-03-25 02:16:33.830] [fileLog] [info] quantification processed 55000000 fragments so far [2022-03-25 02:16:35.187] [fileLog] [info] quantification processed 56000000 fragments so far [2022-03-25 02:16:36.386] [fileLog] [info] quantification processed 57000000 fragments so far [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.80% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 20.40% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 12.20% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.90% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.20% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.10% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 12.80% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 20.10% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.00% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 23.80% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.20% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 11.10% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 13.60% zero probability fragments [2022-03-25 02:16:36.871] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments [2022-03-25 02:16:36.872] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments [2022-03-25 02:16:36.872] [jointLog] [info] Thread saw mini-batch with a maximum of 11.70% zero probability fragments [2022-03-25 02:16:36.872] [jointLog] [info] Thread saw mini-batch with a maximum of 10.90% zero probability fragments [2022-03-25 02:16:36.873] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments [2022-03-25 02:16:36.874] [jointLog] [info] Thread saw mini-batch with a maximum of 23.40% zero probability fragments [2022-03-25 02:16:36.875] [jointLog] [info] Completed first pass through the alignment file. Total # of mapped reads : 57400280 # of uniquely mapped reads : 46589447 # ambiguously mapped reads : 10810833 [2022-03-25 02:16:36.910] [jointLog] [info] Computed 56016 rich equivalence classes for further processing [2022-03-25 02:16:36.910] [jointLog] [info] Counted 56732693 total reads in the equivalence classes [2022-03-25 02:16:36.911] [jointLog] [info] starting optimizer [2022-03-25 02:16:36.929] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2022-03-25 02:16:36.931] [jointLog] [info] iteration = 0 | max rel diff. = 232.439 [2022-03-25 02:16:36.871] [fileLog] [info] quantification processed 57400280 fragments so far [2022-03-25 02:16:37.171] [jointLog] [info] iteration = 100 | max rel diff. = 2.19103 [2022-03-25 02:16:37.397] [jointLog] [info] iteration = 200 | max rel diff. = 0.091545 [2022-03-25 02:16:37.622] [jointLog] [info] iteration = 300 | max rel diff. = 0.0651082 [2022-03-25 02:16:37.847] [jointLog] [info] iteration = 400 | max rel diff. = 0.347708 [2022-03-25 02:16:38.071] [jointLog] [info] iteration = 500 | max rel diff. = 0.168539 [2022-03-25 02:16:38.295] [jointLog] [info] iteration = 600 | max rel diff. = 0.0500836 [2022-03-25 02:16:38.518] [jointLog] [info] iteration = 700 | max rel diff. = 0.0422371 [2022-03-25 02:16:38.746] [jointLog] [info] iteration = 800 | max rel diff. = 0.0260522 [2022-03-25 02:16:38.824] [jointLog] [info] iteration = 836 | max rel diff. = 0.00739265 [2022-03-25 02:16:38.828] [jointLog] [info] finished optimizer [2022-03-25 02:16:38.828] [jointLog] [info] writing output [2022-03-25 02:16:40.287] [jointLog] [info] Computing gene-level abundance estimates [2022-03-25 02:16:44.760] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes [2022-03-25 02:16:44.760] [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 02:16:44.813] [jointLog] [info] Aggregating expressions to gene level [2022-03-25 02:16:44.895] [jointLog] [info] done