[2021-05-13 18:17:55.477] [puff::index::jointLog] [info] Running fixFasta
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604319], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603768], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604592], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605864], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603644], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603804], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604055], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603618], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603316], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605850], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603007], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605143], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603340], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603359], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604735], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603379], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604309], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604234], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603739], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604564], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603303], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605430], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605685], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000603725], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000605709], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.483] [puff::index::jointLog] [warning] Entry with header [ENST00000604111], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.579] [puff::index::jointLog] [warning] Entry with header [ENST00000489969], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.842] [puff::index::jointLog] [warning] Entry with header [ENST00000551948], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:55.879] [puff::index::jointLog] [warning] Entry with header [ENST00000550409], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:57.307] [puff::index::jointLog] [warning] Entry with header [ENST00000595481], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:57.792] [puff::index::jointLog] [warning] Entry with header [ENST00000552580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:58.239] [puff::index::jointLog] [warning] Entry with header [ENST00000598624], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:58.548] [puff::index::jointLog] [warning] Entry with header [ENST00000602572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:58.914] [puff::index::jointLog] [warning] Entry with header [ENST00000548090], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:59.580] [puff::index::jointLog] [warning] Entry with header [ENST00000437226], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:59.726] [puff::index::jointLog] [warning] Entry with header [ENST00000417283], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:59.726] [puff::index::jointLog] [warning] Entry with header [ENST00000465958], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:17:59.946] [puff::index::jointLog] [warning] Entry with header [ENST00000594394], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:00.047] [puff::index::jointLog] [warning] Entry with header [ENST00000552241], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:00.077] [puff::index::jointLog] [warning] Entry with header [ENST00000598940], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:01.693] [puff::index::jointLog] [warning] Entry with header [ENST00000552194], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.545] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.546] [puff::index::jointLog] [warning] Entry with header [ENST00000605343], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.756] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.786] [puff::index::jointLog] [warning] Entry with header [ENST00000606517], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.787] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.827] [puff::index::jointLog] [warning] Entry with header [ENST00000573437], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.944] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:02.973] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:56.917] [puff::index::jointLog] [warning] Removed 12985 transcripts that were sequence duplicates of indexed transcripts.
[2021-05-13 18:18:56.917] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-05-13 18:18:57.307] [puff::index::jointLog] [info] Replaced 239850802 non-ATCG nucleotides
[2021-05-13 18:18:57.307] [puff::index::jointLog] [info] Clipped poly-A tails from 1401 transcripts
[2021-05-13 18:19:28.041] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-05-13 18:19:59.505] [puff::index::jointLog] [info] ntHll estimated 2707933202 distinct k-mers, setting filter size to 2^36
[2021-05-13 20:24:03.462] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-05-13 20:24:03.462] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/salmon_sa_index/default
[2021-05-13 20:24:10.138] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-05-13 20:24:10.689] [puff::index::jointLog] [info] contig count for validation: 36156282
[2021-05-13 20:24:28.775] [puff::index::jointLog] [info] Total # of Contigs : 36156282
[2021-05-13 20:24:28.775] [puff::index::jointLog] [info] Total # of numerical Contigs : 36156282
[2021-05-13 20:24:30.770] [puff::index::jointLog] [info] Total # of contig vec entries: 321803270
[2021-05-13 20:24:30.770] [puff::index::jointLog] [info] bits per offset entry 29
[2021-05-13 20:24:52.649] [puff::index::jointLog] [info] Done constructing the contig vector. 36156283
[2021-05-13 20:25:25.306] [puff::index::jointLog] [info] # segments = 36156282
[2021-05-13 20:25:25.306] [puff::index::jointLog] [info] total length = 3823636891
[2021-05-13 20:25:25.542] [puff::index::jointLog] [info] Reading the reference files ...
[2021-05-13 20:25:40.835] [puff::index::jointLog] [info] positional integer width = 32
[2021-05-13 20:25:40.835] [puff::index::jointLog] [info] seqSize = 3823636891
[2021-05-13 20:25:40.835] [puff::index::jointLog] [info] rankSize = 3823636891
[2021-05-13 20:25:40.835] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-05-13 20:25:40.835] [puff::index::jointLog] [info] num keys = 2738948431
[2021-05-13 20:34:42.156] [puff::index::jointLog] [info] mphf size = 1710.88 MB
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk size = 477954612
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 0 = [0, 477954612)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 1 = [477954612, 955909234)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 2 = [955909234, 1433863846)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 3 = [1433863846, 1911818458)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 4 = [1911818458, 2389773070)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 5 = [2389773070, 2867727695)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 6 = [2867727695, 3345682307)
[2021-05-13 20:34:42.157] [puff::index::jointLog] [info] chunk 7 = [3345682307, 3823636861)
[2021-05-13 20:47:03.167] [puff::index::jointLog] [info] finished populating pos vector
[2021-05-13 20:47:03.167] [puff::index::jointLog] [info] writing index components
[2021-05-13 20:48:36.213] [puff::index::jointLog] [info] finished writing dense pufferfish index