[2021-05-13 18:17:54.038] [puff::index::jointLog] [info] Running fixFasta
[2021-05-13 18:17:55.352] [puff::index::jointLog] [warning] Entry with header [ENSRNOT00000085980.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.512] [puff::index::jointLog] [warning] Entry with header [ENSRNOT00000093397.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:43.886] [puff::index::jointLog] [warning] Removed 521 transcripts that were sequence duplicates of indexed transcripts.
[2021-05-13 18:18:43.886] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-05-13 18:18:43.886] [puff::index::jointLog] [warning] There were 2 duplicate decoy sequences.
[2021-05-13 18:18:43.895] [puff::index::jointLog] [info] Replaced 140324814 non-ATCG nucleotides
[2021-05-13 18:18:43.895] [puff::index::jointLog] [info] Clipped poly-A tails from 58 transcripts
[2021-05-13 18:19:09.168] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-05-13 18:19:35.557] [puff::index::jointLog] [info] ntHll estimated 2411746066 distinct k-mers, setting filter size to 2^36
[2021-05-13 19:38:55.016] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-05-13 19:38:55.017] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/salmon_sa_index/default
[2021-05-13 19:39:00.779] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-05-13 19:39:01.152] [puff::index::jointLog] [info] contig count for validation: 24844458
[2021-05-13 19:39:17.250] [puff::index::jointLog] [info] Total # of Contigs : 24844458
[2021-05-13 19:39:17.250] [puff::index::jointLog] [info] Total # of numerical Contigs : 24844458
[2021-05-13 19:39:18.620] [puff::index::jointLog] [info] Total # of contig vec entries: 268543925
[2021-05-13 19:39:18.620] [puff::index::jointLog] [info] bits per offset entry 29
[2021-05-13 19:39:33.846] [puff::index::jointLog] [info] Done constructing the contig vector. 24844459
[2021-05-13 19:40:09.480] [puff::index::jointLog] [info] # segments = 24844458
[2021-05-13 19:40:09.480] [puff::index::jointLog] [info] total length = 3171654430
[2021-05-13 19:40:09.661] [puff::index::jointLog] [info] Reading the reference files ...
[2021-05-13 19:40:26.934] [puff::index::jointLog] [info] positional integer width = 32
[2021-05-13 19:40:26.934] [puff::index::jointLog] [info] seqSize = 3171654430
[2021-05-13 19:40:26.934] [puff::index::jointLog] [info] rankSize = 3171654430
[2021-05-13 19:40:26.934] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-05-13 19:40:26.934] [puff::index::jointLog] [info] num keys = 2426320690
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] mphf size = 1515.54 MB
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk size = 396456804
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 0 = [0, 396456804)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 1 = [396456804, 792913608)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 2 = [792913608, 1189370412)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 3 = [1189370412, 1585827242)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 4 = [1585827242, 1982284046)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 5 = [1982284046, 2378740850)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 6 = [2378740850, 2775197654)
[2021-05-13 19:48:22.938] [puff::index::jointLog] [info] chunk 7 = [2775197654, 3171654400)
[2021-05-13 19:59:22.913] [puff::index::jointLog] [info] finished populating pos vector
[2021-05-13 19:59:22.913] [puff::index::jointLog] [info] writing index components
[2021-05-13 20:00:19.389] [puff::index::jointLog] [info] finished writing dense pufferfish index