[2022-03-25 01:50:05.288] [jointLog] [info] setting maxHashResizeThreads to 28 [2022-03-25 01:50:05.288] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-03-25 01:50:05.289] [jointLog] [info] numQuantThreads = 22 [2022-03-25 01:50:06.336] [jointLog] [info] replaced 15020 non-ACGT nucleotides with random nucleotides [2022-03-25 01:50:06.499] [fileLog] [info] quantification processed 0 fragments so far [2022-03-25 01:50:07.636] [fileLog] [info] quantification processed 1000000 fragments so far [2022-03-25 01:50:08.924] [fileLog] [info] quantification processed 2000000 fragments so far [2022-03-25 01:50:09.755] [jointLog] [info] The alignment group queue pool has been exhausted. 557839 extra fragments were allocated on the heap to saturate the pool. No new fragments will be allocated [2022-03-25 01:50:11.523] [fileLog] [info] quantification processed 3000000 fragments so far [2022-03-25 01:50:16.441] [fileLog] [info] quantification processed 4000000 fragments so far [2022-03-25 01:50:21.381] [fileLog] [info] quantification processed 5000000 fragments so far [2022-03-25 01:50:26.290] [fileLog] [info] quantification processed 6000000 fragments so far [2022-03-25 01:50:31.188] [fileLog] [info] quantification processed 7000000 fragments so far [2022-03-25 01:50:32.284] [fileLog] [info] quantification processed 8000000 fragments so far [2022-03-25 01:50:33.451] [fileLog] [info] quantification processed 9000000 fragments so far [2022-03-25 01:50:34.830] [fileLog] [info] quantification processed 10000000 fragments so far [2022-03-25 01:50:36.300] [fileLog] [info] quantification processed 11000000 fragments so far [2022-03-25 01:50:38.681] [fileLog] [info] quantification processed 12000000 fragments so far [2022-03-25 01:50:40.978] [fileLog] [info] quantification processed 13000000 fragments so far [2022-03-25 01:50:42.479] [fileLog] [info] quantification processed 14000000 fragments so far [2022-03-25 01:50:42.674] [fileLog] [info] quantification processed 14130706 fragments so far [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.80% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.70% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.40% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 9.90% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.90% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.00% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.90% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.00% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 14.60% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.30% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 10.90% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.30% zero probability fragments [2022-03-25 01:50:42.675] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 01:50:42.676] [jointLog] [info] Thread saw mini-batch with a maximum of 13.60% zero probability fragments [2022-03-25 01:50:42.678] [jointLog] [info] Thread saw mini-batch with a maximum of 14.00% zero probability fragments [2022-03-25 01:50:42.679] [jointLog] [info] Thread saw mini-batch with a maximum of 11.70% zero probability fragments [2022-03-25 01:50:42.683] [jointLog] [info] Thread saw mini-batch with a maximum of 12.80% zero probability fragments [2022-03-25 01:50:42.684] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 01:50:42.685] [jointLog] [info] Thread saw mini-batch with a maximum of 11.50% zero probability fragments [2022-03-25 01:50:42.685] [jointLog] [info] Completed first pass through the alignment file. Total # of mapped reads : 14130706 # of uniquely mapped reads : 11372470 # ambiguously mapped reads : 2758236 [2022-03-25 01:50:42.712] [jointLog] [info] Computed 33751 rich equivalence classes for further processing [2022-03-25 01:50:42.712] [jointLog] [info] Counted 13894334 total reads in the equivalence classes [2022-03-25 01:50:42.713] [jointLog] [info] starting optimizer [2022-03-25 01:50:42.729] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2022-03-25 01:50:42.732] [jointLog] [info] iteration = 0 | max rel diff. = 22542.2 [2022-03-25 01:50:42.962] [jointLog] [info] iteration = 100 | max rel diff. = 6.73116 [2022-03-25 01:50:43.183] [jointLog] [info] iteration = 200 | max rel diff. = 0.494383 [2022-03-25 01:50:43.401] [jointLog] [info] iteration = 300 | max rel diff. = 0.816262 [2022-03-25 01:50:43.618] [jointLog] [info] iteration = 400 | max rel diff. = 1.46615 [2022-03-25 01:50:43.835] [jointLog] [info] iteration = 500 | max rel diff. = 0.46224 [2022-03-25 01:50:44.055] [jointLog] [info] iteration = 600 | max rel diff. = 0.499374 [2022-03-25 01:50:44.268] [jointLog] [info] iteration = 700 | max rel diff. = 0.0256699 [2022-03-25 01:50:44.481] [jointLog] [info] iteration = 800 | max rel diff. = 0.062196 [2022-03-25 01:50:44.694] [jointLog] [info] iteration = 900 | max rel diff. = 0.0132841 [2022-03-25 01:50:44.901] [jointLog] [info] iteration = 998 | max rel diff. = 0.00711345 [2022-03-25 01:50:44.907] [jointLog] [info] finished optimizer [2022-03-25 01:50:44.907] [jointLog] [info] writing output [2022-03-25 01:50:46.285] [jointLog] [info] Computing gene-level abundance estimates [2022-03-25 01:50:50.729] [jointLog] [info] There were 38326 transcripts mapping to 34947 genes [2022-03-25 01:50:50.730] [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 01:50:50.784] [jointLog] [info] Aggregating expressions to gene level [2022-03-25 01:50:50.863] [jointLog] [info] done