[2021-04-08 12:55:48.352] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.359] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.360] [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 12:55:48.436] [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 12:55:48.669] [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 12:55:48.702] [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 12:55:49.990] [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 12:55:50.459] [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 12:55:50.883] [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 12:55:51.179] [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 12:55:51.528] [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 12:55:52.156] [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 12:55:52.294] [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 12:55:52.294] [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 12:55:52.504] [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 12:55:52.600] [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 12:55:52.627] [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 12:55:54.115] [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 12:55:54.919] [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 12:55:54.919] [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 12:55:55.114] [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 12:55:55.143] [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 12:55:55.143] [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 12:55:55.181] [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 12:55:55.270] [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 12:55:55.288] [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 12:55:57.355] [puff::index::jointLog] [warning] Removed 12985 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 12:55:57.355] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 12:55:57.370] [puff::index::jointLog] [info] Replaced 20 non-ATCG nucleotides
[2021-04-08 12:55:57.371] [puff::index::jointLog] [info] Clipped poly-A tails from 1401 transcripts
[2021-04-08 12:55:59.660] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 12:56:03.183] [puff::index::jointLog] [info] ntHll estimated 150521489 distinct k-mers, setting filter size to 2^32
[2021-04-08 12:58:06.109] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 12:58:06.109] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/salmon_partial_sa_index/default
[2021-04-08 12:58:06.495] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 12:58:06.508] [puff::index::jointLog] [info] contig count for validation: 1665554
[2021-04-08 12:58:07.255] [puff::index::jointLog] [info] Total # of Contigs : 1665554
[2021-04-08 12:58:07.255] [puff::index::jointLog] [info] Total # of numerical Contigs : 1665554
[2021-04-08 12:58:07.375] [puff::index::jointLog] [info] Total # of contig vec entries: 9928388
[2021-04-08 12:58:07.375] [puff::index::jointLog] [info] bits per offset entry 24
[2021-04-08 12:58:08.074] [puff::index::jointLog] [info] Done constructing the contig vector. 1665555
[2021-04-08 12:58:09.961] [puff::index::jointLog] [info] # segments = 1665554
[2021-04-08 12:58:09.961] [puff::index::jointLog] [info] total length = 201888185
[2021-04-08 12:58:10.059] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 12:58:11.734] [puff::index::jointLog] [info] positional integer width = 28
[2021-04-08 12:58:11.734] [puff::index::jointLog] [info] seqSize = 201888185
[2021-04-08 12:58:11.734] [puff::index::jointLog] [info] rankSize = 201888185
[2021-04-08 12:58:11.734] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 12:58:11.734] [puff::index::jointLog] [info] num keys = 151921565
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] mphf size = 94.8937 MB
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk size = 25236024
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 0 = [0, 25236024)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 1 = [25236024, 50472071)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 2 = [50472071, 75708107)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 3 = [75708107, 100944131)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 4 = [100944131, 126180185)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 5 = [126180185, 151416227)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 6 = [151416227, 176652251)
[2021-04-08 12:58:19.017] [puff::index::jointLog] [info] chunk 7 = [176652251, 201888155)
[2021-04-08 12:58:26.767] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 12:58:26.767] [puff::index::jointLog] [info] writing index components
[2021-04-08 12:58:30.603] [puff::index::jointLog] [info] finished writing dense pufferfish index