[2021-04-08 16:06:06.015] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.029] [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)
[2021-04-08 16:06:06.130] [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)
[2021-04-08 16:06:06.409] [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)
[2021-04-08 16:06:06.447] [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)
[2021-04-08 16:06:08.001] [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)
[2021-04-08 16:06:08.534] [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)
[2021-04-08 16:06:09.025] [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)
[2021-04-08 16:06:09.384] [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)
[2021-04-08 16:06:09.776] [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)
[2021-04-08 16:06:10.478] [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)
[2021-04-08 16:06:10.632] [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)
[2021-04-08 16:06:10.632] [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)
[2021-04-08 16:06:10.860] [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)
[2021-04-08 16:06:10.965] [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)
[2021-04-08 16:06:10.998] [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)
[2021-04-08 16:06:12.715] [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)
[2021-04-08 16:06:13.632] [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)
[2021-04-08 16:06:13.634] [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)
[2021-04-08 16:06:13.850] [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)
[2021-04-08 16:06:13.882] [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)
[2021-04-08 16:06:13.883] [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)
[2021-04-08 16:06:13.925] [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)
[2021-04-08 16:06:14.021] [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)
[2021-04-08 16:06:14.038] [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)
[2021-04-08 16:06:14.084] [puff::index::jointLog] [warning] Removed 12985 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:06:14.084] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:06:14.143] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2021-04-08 16:06:14.143] [puff::index::jointLog] [info] Clipped poly-A tails from 1401 transcripts
[2021-04-08 16:06:16.635] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:06:18.949] [puff::index::jointLog] [info] ntHll estimated 100826112 distinct k-mers, setting filter size to 2^31
[2021-04-08 16:55:14.915] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:55:14.915] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default
[2021-04-08 16:55:15.162] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:55:15.170] [puff::index::jointLog] [info] contig count for validation: 994040
[2021-04-08 16:55:15.542] [puff::index::jointLog] [info] Total # of Contigs : 994040
[2021-04-08 16:55:15.542] [puff::index::jointLog] [info] Total # of numerical Contigs : 994040
[2021-04-08 16:55:15.603] [puff::index::jointLog] [info] Total # of contig vec entries: 5131470
[2021-04-08 16:55:15.603] [puff::index::jointLog] [info] bits per offset entry 23
[2021-04-08 16:55:15.859] [puff::index::jointLog] [info] Done constructing the contig vector. 994041
[2021-04-08 16:55:16.511] [puff::index::jointLog] [info] # segments = 994040
[2021-04-08 16:55:16.511] [puff::index::jointLog] [info] total length = 131267297
[2021-04-08 16:55:16.566] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:55:17.855] [puff::index::jointLog] [info] positional integer width = 27
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] seqSize = 131267297
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] rankSize = 131267297
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] num keys = 101446097
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] mphf size = 63.3658 MB
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk size = 16408413
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 0 = [0, 16408413)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 1 = [16408413, 32816826)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 2 = [32816826, 49225239)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 3 = [49225239, 65633652)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 4 = [65633652, 82042065)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 5 = [82042065, 98450490)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 6 = [98450490, 114858903)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 7 = [114858903, 131267267)
[2021-04-08 16:56:00.078] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:56:00.078] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:56:01.864] [puff::index::jointLog] [info] finished writing dense pufferfish index