[2023-03-28 15:17:46.129] [puff::index::jointLog] [info] Running fixFasta
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000182373], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000193530], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000184666], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000181734], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000183389], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000187118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.725] [puff::index::jointLog] [warning] Entry with header [ENSDART00000181843], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.911] [puff::index::jointLog] [warning] Entry with header [ENSDART00000192604], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.980] [puff::index::jointLog] [warning] Entry with header [ENSDART00000189431], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:46.980] [puff::index::jointLog] [warning] Entry with header [ENSDART00000189226], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:47.663] [puff::index::jointLog] [warning] Entry with header [ENSDART00000188264], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:48.212] [puff::index::jointLog] [warning] Entry with header [ENSDART00000183775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:48.257] [puff::index::jointLog] [warning] Entry with header [ENSDART00000186673], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:17:48.418] [puff::index::jointLog] [warning] Entry with header [ENSDART00000190391], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:11.713] [puff::index::jointLog] [warning] Removed 441 transcripts that were sequence duplicates of indexed transcripts.
[2023-03-28 15:18:11.713] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2023-03-28 15:18:11.718] [puff::index::jointLog] [info] Replaced 4704404 non-ATCG nucleotides
[2023-03-28 15:18:11.718] [puff::index::jointLog] [info] Clipped poly-A tails from 383 transcripts
[2023-03-28 15:18:13.915] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2023-03-28 15:18:24.729] [puff::index::jointLog] [info] ntHll estimated 1076544936 distinct k-mers, setting filter size to 2^35
[2023-03-28 16:23:35.498] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2023-03-28 16:23:35.498] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory SalmonIndex
[2023-03-28 16:23:38.837] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2023-03-28 16:23:39.273] [puff::index::jointLog] [info] contig count for validation: 24973729
[2023-03-28 16:23:50.747] [puff::index::jointLog] [info] Total # of Contigs : 24973729
[2023-03-28 16:23:50.747] [puff::index::jointLog] [info] Total # of numerical Contigs : 24973729
[2023-03-28 16:23:51.744] [puff::index::jointLog] [info] Total # of contig vec entries: 215438803
[2023-03-28 16:23:51.744] [puff::index::jointLog] [info] bits per offset entry 28
[2023-03-28 16:23:57.500] [puff::index::jointLog] [info] Done constructing the contig vector. 24973730
[2023-03-28 16:24:11.143] [puff::index::jointLog] [info] # segments = 24973729
[2023-03-28 16:24:11.143] [puff::index::jointLog] [info] total length = 1832569942
[2023-03-28 16:24:11.233] [puff::index::jointLog] [info] Reading the reference files ...
[2023-03-28 16:24:16.587] [puff::index::jointLog] [info] positional integer width = 31
[2023-03-28 16:24:16.587] [puff::index::jointLog] [info] seqSize = 1832569942
[2023-03-28 16:24:16.587] [puff::index::jointLog] [info] rankSize = 1832569942
[2023-03-28 16:24:16.587] [puff::index::jointLog] [info] edgeVecSize = 0
[2023-03-28 16:24:16.587] [puff::index::jointLog] [info] num keys = 1083358072
[2023-03-28 16:27:42.370] [puff::index::jointLog] [info] mphf size = 676.717 MB
[2023-03-28 16:27:43.197] [puff::index::jointLog] [info] chunk size = 1832569942
[2023-03-28 16:27:43.198] [puff::index::jointLog] [info] chunk 0 = [0, 1832569912)
[2023-03-28 16:32:20.626] [puff::index::jointLog] [info] finished populating pos vector
[2023-03-28 16:32:20.626] [puff::index::jointLog] [info] writing index components
[2023-03-28 16:32:27.948] [puff::index::jointLog] [info] finished writing dense pufferfish index