[2021-05-13 18:18:15.058] [puff::index::jointLog] [info] Running fixFasta
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000631435.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000415118.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000448914.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000434970.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632684.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000439842.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390567.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000452198.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390569.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000437320.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390571.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390572.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390574.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390575.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000431870.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000450276.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390578.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000451044.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390580.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390581.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000431440.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390583.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633210.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000603693.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000604838.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000604446.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000604102.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000603935.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632524.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633009.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000634070.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632963.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633030.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633765.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632619.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000631871.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633010.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633159.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632473.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000631884.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632859.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000631895.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000634154.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632609.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632911.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633504.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632304.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000632542.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000634085.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000633353.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000631803.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390584.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390585.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000430425.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000454691.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390588.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000414852.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390590.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000390591.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000454908.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000604642.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000603326.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000604950.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000603077.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.063] [puff::index::jointLog] [warning] Entry with header [ENST00000605284.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:15.637] [puff::index::jointLog] [warning] Entry with header [ENST00000629250.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:16.188] [puff::index::jointLog] [warning] Entry with header [ENST00000632054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:16.493] [puff::index::jointLog] [warning] Entry with header [ENST00000437226.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:18.095] [puff::index::jointLog] [warning] Entry with header [ENST00000626807.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:20.437] [puff::index::jointLog] [warning] Entry with header [ENST00000417283.5], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:20.437] [puff::index::jointLog] [warning] Entry with header [ENST00000465958.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.181] [puff::index::jointLog] [warning] Entry with header [ENST00000632342.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.181] [puff::index::jointLog] [warning] Entry with header [ENST00000518246.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.328] [puff::index::jointLog] [warning] Entry with header [ENST00000543745.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.347] [puff::index::jointLog] [warning] Entry with header [ENST00000473810.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.477] [puff::index::jointLog] [warning] Entry with header [ENST00000579054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.486] [puff::index::jointLog] [warning] Entry with header [ENST00000603775.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.643] [puff::index::jointLog] [warning] Entry with header [ENST00000573437.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:18:22.670] [puff::index::jointLog] [warning] Entry with header [ENST00000634174.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-05-13 18:19:11.618] [puff::index::jointLog] [warning] Removed 11698 transcripts that were sequence duplicates of indexed transcripts.
[2021-05-13 18:19:11.618] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-05-13 18:19:11.813] [puff::index::jointLog] [info] Replaced 165046095 non-ATCG nucleotides
[2021-05-13 18:19:11.813] [puff::index::jointLog] [info] Clipped poly-A tails from 1439 transcripts
[2021-05-13 18:19:38.951] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-05-13 18:20:08.056] [puff::index::jointLog] [info] ntHll estimated 2640457023 distinct k-mers, setting filter size to 2^36
[2021-05-13 20:24:48.987] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-05-13 20:24:48.987] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index/default
[2021-05-13 20:24:55.617] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-05-13 20:24:56.211] [puff::index::jointLog] [info] contig count for validation: 36981177
[2021-05-13 20:25:16.933] [puff::index::jointLog] [info] Total # of Contigs : 36981177
[2021-05-13 20:25:16.933] [puff::index::jointLog] [info] Total # of numerical Contigs : 36981177
[2021-05-13 20:25:19.094] [puff::index::jointLog] [info] Total # of contig vec entries: 360587850
[2021-05-13 20:25:19.094] [puff::index::jointLog] [info] bits per offset entry 29
[2021-05-13 20:25:41.800] [puff::index::jointLog] [info] Done constructing the contig vector. 36981178
[2021-05-13 20:26:16.007] [puff::index::jointLog] [info] # segments = 36981177
[2021-05-13 20:26:16.007] [puff::index::jointLog] [info] total length = 3784352032
[2021-05-13 20:26:16.255] [puff::index::jointLog] [info] Reading the reference files ...
[2021-05-13 20:26:30.953] [puff::index::jointLog] [info] positional integer width = 32
[2021-05-13 20:26:30.953] [puff::index::jointLog] [info] seqSize = 3784352032
[2021-05-13 20:26:30.953] [puff::index::jointLog] [info] rankSize = 3784352032
[2021-05-13 20:26:30.953] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-05-13 20:26:30.953] [puff::index::jointLog] [info] num keys = 2674916722
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] mphf size = 1670.87 MB
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk size = 473044004
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 0 = [0, 473044008)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 1 = [473044008, 946088012)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 2 = [946088012, 1419132016)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 3 = [1419132016, 1892176020)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 4 = [1892176020, 2365220024)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 5 = [2365220024, 2838264028)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 6 = [2838264028, 3311308032)
[2021-05-13 20:35:08.612] [puff::index::jointLog] [info] chunk 7 = [3311308032, 3784352002)
[2021-05-13 20:46:57.727] [puff::index::jointLog] [info] finished populating pos vector
[2021-05-13 20:46:57.727] [puff::index::jointLog] [info] writing index components
[2021-05-13 20:48:25.636] [puff::index::jointLog] [info] finished writing dense pufferfish index