[2021-04-08 16:06:36.723] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000196221.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179664.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000177564.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178537.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178862.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179520.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179883.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000195858.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179932.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000180001.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178815.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000177965.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178909.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000177646.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178230.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178483.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179262.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178549.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000193012.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179166.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179560.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000177839.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000103439.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000180266.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.733] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000103441.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.967] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226153.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:36.971] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000227223.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:37.055] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226615.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:37.176] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000231713.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:37.176] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000231466.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:37.811] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000179793.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:37.815] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000165700.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:38.431] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226961.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:38.491] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000227002.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:39.840] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226589.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:40.019] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000229312.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:40.371] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000228114.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:41.044] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226226.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:41.368] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000226172.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.567] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000103739.3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.619] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000200713.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.642] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000191703.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.779] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000192089.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.779] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178902.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.779] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000170385.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.779] [puff::index::jointLog] [warning] Entry with header [ENSMUST00000178811.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:42.851] [puff::index::jointLog] [warning] Removed 2237 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:06:42.851] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:06:42.865] [puff::index::jointLog] [info] Replaced 3 non-ATCG nucleotides
[2021-04-08 16:06:42.865] [puff::index::jointLog] [info] Clipped poly-A tails from 645 transcripts
[2021-04-08 16:06:44.973] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:06:46.802] [puff::index::jointLog] [info] ntHll estimated 100197723 distinct k-mers, setting filter size to 2^31
[2021-04-08 16:41:17.192] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:41:17.192] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/salmon_index/default
[2021-04-08 16:41:17.427] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:41:17.434] [puff::index::jointLog] [info] contig count for validation: 718163
[2021-04-08 16:41:17.686] [puff::index::jointLog] [info] Total # of Contigs : 718163
[2021-04-08 16:41:17.686] [puff::index::jointLog] [info] Total # of numerical Contigs : 718163
[2021-04-08 16:41:17.725] [puff::index::jointLog] [info] Total # of contig vec entries: 3357576
[2021-04-08 16:41:17.725] [puff::index::jointLog] [info] bits per offset entry 22
[2021-04-08 16:41:17.863] [puff::index::jointLog] [info] Done constructing the contig vector. 718164
[2021-04-08 16:41:18.332] [puff::index::jointLog] [info] # segments = 718163
[2021-04-08 16:41:18.332] [puff::index::jointLog] [info] total length = 122290787
[2021-04-08 16:41:18.375] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:41:19.468] [puff::index::jointLog] [info] positional integer width = 27
[2021-04-08 16:41:19.468] [puff::index::jointLog] [info] seqSize = 122290787
[2021-04-08 16:41:19.468] [puff::index::jointLog] [info] rankSize = 122290787
[2021-04-08 16:41:19.468] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:41:19.468] [puff::index::jointLog] [info] num keys = 100745897
[2021-04-08 16:41:37.094] [puff::index::jointLog] [info] mphf size = 62.9284 MB
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk size = 15286349
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 0 = [0, 15286349)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 1 = [15286349, 30572719)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 2 = [30572719, 45859068)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 3 = [45859068, 61145417)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 4 = [61145417, 76431766)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 5 = [76431766, 91718115)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 6 = [91718115, 107004464)
[2021-04-08 16:41:37.095] [puff::index::jointLog] [info] chunk 7 = [107004464, 122290757)
[2021-04-08 16:42:01.927] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:42:01.928] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:42:04.751] [puff::index::jointLog] [info] finished writing dense pufferfish index