[2020-01-17 01:46:15.237] [puff::index::jointLog] [info] Running fixFasta
[2020-01-17 01:47:36.605] [puff::index::jointLog] [warning] Removed 1185 transcripts that were sequence duplicates of indexed transcripts.
[2020-01-17 01:47:36.605] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-01-17 01:47:36.605] [puff::index::jointLog] [info] Replaced 165046095 non-ATCG nucleotides
[2020-01-17 01:47:36.606] [puff::index::jointLog] [info] Clipped poly-A tails from 13084 transcripts
[2020-01-17 01:47:41.653] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-01-17 01:48:30.811] [puff::index::jointLog] [info] ntHll estimated 2641348574 distinct k-mers, setting filter size to 2^36
[2020-01-17 02:06:28.283] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory grch38_salmon_index
[2020-01-17 02:06:36.982] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-01-17 02:07:00.161] [puff::index::jointLog] [info] contig count for validation: 36862413
[2020-01-17 02:07:49.465] [puff::index::jointLog] [info] Total # of Contigs : 36862413
[2020-01-17 02:07:49.465] [puff::index::jointLog] [info] Total # of numerical Contigs : 36862413
[2020-01-17 02:10:40.544] [puff::index::jointLog] [info] 
Total # of segments we have position for : 36862413
[2020-01-17 02:10:42.657] [puff::index::jointLog] [info] total contig vec entries 365571485
[2020-01-17 02:10:42.657] [puff::index::jointLog] [info] bits per offset entry 29
[2020-01-17 02:11:18.430] [puff::index::jointLog] [info] there were 3206321  equivalence classes
[2020-01-17 02:11:59.946] [puff::index::jointLog] [info] # segments = 36862413
[2020-01-17 02:11:59.946] [puff::index::jointLog] [info] total length = 3781003616
[2020-01-17 02:12:00.187] [puff::index::jointLog] [info] Reading the reference files ...
[2020-01-17 02:12:27.601] [puff::index::jointLog] [info] positional integer width = 32
[2020-01-17 02:12:27.601] [puff::index::jointLog] [info] seqSize = 3781003616
[2020-01-17 02:12:27.601] [puff::index::jointLog] [info] rankSize = 3781003616
[2020-01-17 02:12:27.601] [puff::index::jointLog] [info] edgeVecSize = 0
[2020-01-17 02:12:27.601] [puff::index::jointLog] [info] num keys = 2675131226
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] mphf size = 1671.01 MB
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk size = 157541818
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 0 = [0, 157541818)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 1 = [157541818, 315083641)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 2 = [315083641, 472625485)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 3 = [472625485, 630167303)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 4 = [630167303, 787709121)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 5 = [787709121, 945250939)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 6 = [945250939, 1102792759)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 7 = [1102792759, 1260334577)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 8 = [1260334577, 1417876395)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 9 = [1417876395, 1575418213)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 10 = [1575418213, 1732960031)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 11 = [1732960031, 1890501849)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 12 = [1890501849, 2048043667)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 13 = [2048043667, 2205585485)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 14 = [2205585485, 2363127311)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 15 = [2363127311, 2520669129)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 16 = [2520669129, 2678210947)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 17 = [2678210947, 2835752765)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 18 = [2835752765, 2993294583)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 19 = [2993294583, 3150836401)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 20 = [3150836401, 3308378219)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 21 = [3308378219, 3465920037)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 22 = [3465920037, 3623461855)
[2020-01-17 02:13:32.923] [puff::index::jointLog] [info] chunk 23 = [3623461855, 3781003586)
[2020-01-17 02:14:34.295] [puff::index::jointLog] [info] finished populating pos vector
[2020-01-17 02:14:34.295] [puff::index::jointLog] [info] writing index components
[2020-01-17 02:14:54.530] [puff::index::jointLog] [info] finished writing dense pufferfish index