[2022-03-24 18:42:17.704] [puff::index::jointLog] [info] Running fixFasta
[2022-03-24 18:42:38.710] [puff::index::jointLog] [warning] Removed 292 transcripts that were sequence duplicates of indexed transcripts.
[2022-03-24 18:42:38.710] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2022-03-24 18:42:38.712] [puff::index::jointLog] [info] Replaced 158507060 non-ATCG nucleotides
[2022-03-24 18:42:38.712] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
[2022-03-24 18:42:39.799] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-03-24 18:42:48.793] [puff::index::jointLog] [info] ntHll estimated 829529786 distinct k-mers, setting filter size to 2^34
[2022-03-24 18:47:07.006] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-03-24 18:47:07.006] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory salmon
[2022-03-24 18:47:09.506] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-03-24 18:47:09.695] [puff::index::jointLog] [info] contig count for validation: 12095405
[2022-03-24 18:47:14.027] [puff::index::jointLog] [info] Total # of Contigs : 12095405
[2022-03-24 18:47:14.027] [puff::index::jointLog] [info] Total # of numerical Contigs : 12095405
[2022-03-24 18:47:14.348] [puff::index::jointLog] [info] Total # of contig vec entries: 65205736
[2022-03-24 18:47:14.348] [puff::index::jointLog] [info] bits per offset entry 26
[2022-03-24 18:47:17.989] [puff::index::jointLog] [info] Done constructing the contig vector. 12095406
[2022-03-24 18:47:23.139] [puff::index::jointLog] [info] # segments = 12095405
[2022-03-24 18:47:23.139] [puff::index::jointLog] [info] total length = 1195465780
[2022-03-24 18:47:23.216] [puff::index::jointLog] [info] Reading the reference files ...
[2022-03-24 18:47:27.347] [puff::index::jointLog] [info] positional integer width = 31
[2022-03-24 18:47:27.347] [puff::index::jointLog] [info] seqSize = 1195465780
[2022-03-24 18:47:27.347] [puff::index::jointLog] [info] rankSize = 1195465780
[2022-03-24 18:47:27.347] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-03-24 18:47:27.347] [puff::index::jointLog] [info] num keys = 832603630
[2022-03-24 18:47:41.965] [puff::index::jointLog] [info] mphf size = 520.06 MB
[2022-03-24 18:47:42.834] [puff::index::jointLog] [info] chunk size = 42695207
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 0 = [0, 42695229)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 1 = [42695229, 85390436)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 2 = [85390436, 128085667)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 3 = [128085667, 170780874)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 4 = [170780874, 213476104)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 5 = [213476104, 256171311)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 6 = [256171311, 298866518)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 7 = [298866518, 341561725)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 8 = [341561725, 384256959)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 9 = [384256959, 426952166)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 10 = [426952166, 469647384)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 11 = [469647384, 512342591)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 12 = [512342591, 555037798)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 13 = [555037798, 597733005)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 14 = [597733005, 640428226)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 15 = [640428226, 683123433)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 16 = [683123433, 725818648)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 17 = [725818648, 768513855)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 18 = [768513855, 811209062)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 19 = [811209062, 853904269)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 20 = [853904269, 896599476)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 21 = [896599476, 939294683)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 22 = [939294683, 981989890)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 23 = [981989890, 1024685097)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 24 = [1024685097, 1067380304)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 25 = [1067380304, 1110075511)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 26 = [1110075511, 1152770718)
[2022-03-24 18:47:42.835] [puff::index::jointLog] [info] chunk 27 = [1152770718, 1195465750)
[2022-03-24 18:47:53.540] [puff::index::jointLog] [info] finished populating pos vector
[2022-03-24 18:47:53.541] [puff::index::jointLog] [info] writing index components
[2022-03-24 18:47:55.406] [puff::index::jointLog] [info] finished writing dense pufferfish index