[2021-05-13 18:17:54.032] [puff::index::jointLog] [info] Running fixFasta
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.135] [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)
[2021-05-13 18:17:54.338] [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)
[2021-05-13 18:17:54.341] [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)
[2021-05-13 18:17:54.415] [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)
[2021-05-13 18:17:54.522] [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)
[2021-05-13 18:17:54.522] [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)
[2021-05-13 18:17:55.077] [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)
[2021-05-13 18:17:55.080] [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)
[2021-05-13 18:17:55.673] [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)
[2021-05-13 18:17:55.729] [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)
[2021-05-13 18:17:56.993] [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)
[2021-05-13 18:17:57.151] [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)
[2021-05-13 18:17:57.481] [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)
[2021-05-13 18:17:58.109] [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)
[2021-05-13 18:17:58.408] [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)
[2021-05-13 18:17:59.518] [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)
[2021-05-13 18:17:59.568] [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)
[2021-05-13 18:17:59.591] [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)
[2021-05-13 18:17:59.743] [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)
[2021-05-13 18:17:59.743] [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)
[2021-05-13 18:17:59.743] [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)
[2021-05-13 18:17:59.743] [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)
[2021-05-13 18:18:43.908] [puff::index::jointLog] [warning] Removed 2237 transcripts that were sequence duplicates of indexed transcripts.
[2021-05-13 18:18:43.908] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-05-13 18:18:43.929] [puff::index::jointLog] [info] Replaced 78088277 non-ATCG nucleotides
[2021-05-13 18:18:43.929] [puff::index::jointLog] [info] Clipped poly-A tails from 645 transcripts
[2021-05-13 18:19:09.661] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-05-13 18:19:36.530] [puff::index::jointLog] [info] ntHll estimated 2271853738 distinct k-mers, setting filter size to 2^36
[2021-05-13 19:58:37.798] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-05-13 19:58:37.798] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/salmon_sa_index/default
[2021-05-13 19:58:43.362] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-05-13 19:58:43.779] [puff::index::jointLog] [info] contig count for validation: 24942313
[2021-05-13 19:59:04.882] [puff::index::jointLog] [info] Total # of Contigs : 24942313
[2021-05-13 19:59:04.883] [puff::index::jointLog] [info] Total # of numerical Contigs : 24942313
[2021-05-13 19:59:06.561] [puff::index::jointLog] [info] Total # of contig vec entries: 344967281
[2021-05-13 19:59:06.561] [puff::index::jointLog] [info] bits per offset entry 29
[2021-05-13 19:59:28.161] [puff::index::jointLog] [info] Done constructing the contig vector. 24942314
[2021-05-13 20:00:13.314] [puff::index::jointLog] [info] # segments = 24942313
[2021-05-13 20:00:13.314] [puff::index::jointLog] [info] total length = 3023265381
[2021-05-13 20:00:13.521] [puff::index::jointLog] [info] Reading the reference files ...
[2021-05-13 20:00:27.456] [puff::index::jointLog] [info] positional integer width = 32
[2021-05-13 20:00:27.456] [puff::index::jointLog] [info] seqSize = 3023265381
[2021-05-13 20:00:27.456] [puff::index::jointLog] [info] rankSize = 3023265381
[2021-05-13 20:00:27.456] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-05-13 20:00:27.456] [puff::index::jointLog] [info] num keys = 2274995991
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] mphf size = 1421.04 MB
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk size = 377908173
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 0 = [0, 377908173)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 1 = [377908173, 755816346)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 2 = [755816346, 1133724519)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 3 = [1133724519, 1511632720)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 4 = [1511632720, 1889540893)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 5 = [1889540893, 2267449066)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 6 = [2267449066, 2645357239)
[2021-05-13 20:07:48.314] [puff::index::jointLog] [info] chunk 7 = [2645357239, 3023265351)
[2021-05-13 20:17:56.528] [puff::index::jointLog] [info] finished populating pos vector
[2021-05-13 20:17:56.528] [puff::index::jointLog] [info] writing index components
[2021-05-13 20:18:50.411] [puff::index::jointLog] [info] finished writing dense pufferfish index