[2021-04-08 21:09:04.846] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:04.851] [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)
[2021-04-08 21:09:05.409] [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)
[2021-04-08 21:09:05.911] [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)
[2021-04-08 21:09:06.187] [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)
[2021-04-08 21:09:07.700] [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)
[2021-04-08 21:09:09.912] [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)
[2021-04-08 21:09:09.912] [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)
[2021-04-08 21:09:11.574] [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)
[2021-04-08 21:09:11.575] [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)
[2021-04-08 21:09:11.716] [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)
[2021-04-08 21:09:11.734] [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)
[2021-04-08 21:09:11.857] [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)
[2021-04-08 21:09:11.865] [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)
[2021-04-08 21:09:11.969] [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)
[2021-04-08 21:09:11.985] [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)
[2021-04-08 21:09:14.048] [puff::index::jointLog] [warning] Removed 11698 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 21:09:14.048] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 21:09:14.327] [puff::index::jointLog] [info] Replaced 5 non-ATCG nucleotides
[2021-04-08 21:09:14.327] [puff::index::jointLog] [info] Clipped poly-A tails from 1439 transcripts
[2021-04-08 21:09:18.649] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 21:09:22.377] [puff::index::jointLog] [info] ntHll estimated 159634130 distinct k-mers, setting filter size to 2^32
[2021-04-08 21:12:15.288] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 21:12:15.288] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_partial_sa_index/default
[2021-04-08 21:12:15.667] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 21:12:15.681] [puff::index::jointLog] [info] contig count for validation: 1790980
[2021-04-08 21:12:16.400] [puff::index::jointLog] [info] Total # of Contigs : 1790980
[2021-04-08 21:12:16.400] [puff::index::jointLog] [info] Total # of numerical Contigs : 1790980
[2021-04-08 21:12:16.498] [puff::index::jointLog] [info] Total # of contig vec entries: 11692510
[2021-04-08 21:12:16.498] [puff::index::jointLog] [info] bits per offset entry 24
[2021-04-08 21:12:17.095] [puff::index::jointLog] [info] Done constructing the contig vector. 1790981
[2021-04-08 21:12:18.278] [puff::index::jointLog] [info] # segments = 1790980
[2021-04-08 21:12:18.278] [puff::index::jointLog] [info] total length = 215123398
[2021-04-08 21:12:18.348] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 21:12:20.182] [puff::index::jointLog] [info] positional integer width = 28
[2021-04-08 21:12:20.182] [puff::index::jointLog] [info] seqSize = 215123398
[2021-04-08 21:12:20.182] [puff::index::jointLog] [info] rankSize = 215123398
[2021-04-08 21:12:20.182] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 21:12:20.182] [puff::index::jointLog] [info] num keys = 161393998
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] mphf size = 100.81 MB
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk size = 26890425
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 0 = [0, 26890425)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 1 = [26890425, 53780850)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 2 = [53780850, 80671301)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 3 = [80671301, 107561741)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 4 = [107561741, 134452166)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 5 = [134452166, 161342591)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 6 = [161342591, 188233045)
[2021-04-08 21:12:29.445] [puff::index::jointLog] [info] chunk 7 = [188233045, 215123368)
[2021-04-08 21:12:35.499] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 21:12:35.499] [puff::index::jointLog] [info] writing index components
[2021-04-08 21:12:42.690] [puff::index::jointLog] [info] finished writing dense pufferfish index