[2021-04-08 17:59:54.769] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 17:59:55.849] [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)
[2021-04-08 17:59:55.975] [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)
[2021-04-08 17:59:57.102] [puff::index::jointLog] [warning] Removed 519 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 17:59:57.102] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 17:59:57.146] [puff::index::jointLog] [info] Replaced 29727 non-ATCG nucleotides
[2021-04-08 17:59:57.146] [puff::index::jointLog] [info] Clipped poly-A tails from 58 transcripts
[2021-04-08 17:59:57.885] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 17:59:58.993] [puff::index::jointLog] [info] ntHll estimated 81042414 distinct k-mers, setting filter size to 2^31
[2021-04-08 18:00:32.820] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 18:00:32.820] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/salmon_partial_sa_index/default
[2021-04-08 18:00:32.977] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 18:00:32.981] [puff::index::jointLog] [info] contig count for validation: 488784
[2021-04-08 18:00:33.090] [puff::index::jointLog] [info] Total # of Contigs : 488784
[2021-04-08 18:00:33.090] [puff::index::jointLog] [info] Total # of numerical Contigs : 488784
[2021-04-08 18:00:33.102] [puff::index::jointLog] [info] Total # of contig vec entries: 1764412
[2021-04-08 18:00:33.102] [puff::index::jointLog] [info] bits per offset entry 21
[2021-04-08 18:00:33.145] [puff::index::jointLog] [info] Done constructing the contig vector. 488785
[2021-04-08 18:00:33.428] [puff::index::jointLog] [info] # segments = 488784
[2021-04-08 18:00:33.429] [puff::index::jointLog] [info] total length = 95555077
[2021-04-08 18:00:33.443] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 18:00:33.997] [puff::index::jointLog] [info] positional integer width = 27
[2021-04-08 18:00:33.997] [puff::index::jointLog] [info] seqSize = 95555077
[2021-04-08 18:00:33.997] [puff::index::jointLog] [info] rankSize = 95555077
[2021-04-08 18:00:33.997] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 18:00:33.997] [puff::index::jointLog] [info] num keys = 80891557
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] mphf size = 50.527 MB
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk size = 11944385
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 0 = [0, 11944395)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 1 = [11944395, 23888780)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 2 = [23888780, 35833169)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 3 = [35833169, 47777554)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 4 = [47777554, 59721939)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 5 = [59721939, 71666324)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 6 = [71666324, 83610709)
[2021-04-08 18:00:37.024] [puff::index::jointLog] [info] chunk 7 = [83610709, 95555047)
[2021-04-08 18:00:39.686] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 18:00:39.686] [puff::index::jointLog] [info] writing index components
[2021-04-08 18:00:41.072] [puff::index::jointLog] [info] finished writing dense pufferfish index