[2021-04-08 16:07:06.829] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 16:07:08.253] [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 16:07:08.416] [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 16:07:08.746] [puff::index::jointLog] [warning] Removed 519 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:07:08.746] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:07:08.754] [puff::index::jointLog] [info] Replaced 2710 non-ATCG nucleotides
[2021-04-08 16:07:08.754] [puff::index::jointLog] [info] Clipped poly-A tails from 57 transcripts
[2021-04-08 16:07:09.704] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:07:10.332] [puff::index::jointLog] [info] ntHll estimated 50011459 distinct k-mers, setting filter size to 2^30
[2021-04-08 16:16:38.524] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:16:38.524] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default
[2021-04-08 16:16:38.626] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:16:38.628] [puff::index::jointLog] [info] contig count for validation: 150144
[2021-04-08 16:16:38.674] [puff::index::jointLog] [info] Total # of Contigs : 150144
[2021-04-08 16:16:38.674] [puff::index::jointLog] [info] Total # of numerical Contigs : 150144
[2021-04-08 16:16:38.677] [puff::index::jointLog] [info] Total # of contig vec entries: 521380
[2021-04-08 16:16:38.677] [puff::index::jointLog] [info] bits per offset entry 19
[2021-04-08 16:16:38.686] [puff::index::jointLog] [info] Done constructing the contig vector. 150145
[2021-04-08 16:16:38.793] [puff::index::jointLog] [info] # segments = 150144
[2021-04-08 16:16:38.793] [puff::index::jointLog] [info] total length = 54419707
[2021-04-08 16:16:38.805] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] positional integer width = 26
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] seqSize = 54419707
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] rankSize = 54419707
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] num keys = 49915387
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] mphf size = 31.1787 MB
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk size = 6802464
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 0 = [0, 6802464)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 1 = [6802464, 13604928)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 2 = [13604928, 20407392)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 3 = [20407392, 27209856)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 4 = [27209856, 34012320)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 5 = [34012320, 40814784)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 6 = [40814784, 47617248)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 7 = [47617248, 54419677)
[2021-04-08 16:16:58.249] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:16:58.249] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:16:59.138] [puff::index::jointLog] [info] finished writing dense pufferfish index