[2021-04-08 17:35:14.626] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.631] [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 17:35:14.803] [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 17:35:14.806] [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 17:35:14.871] [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 17:35:14.967] [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 17:35:14.967] [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 17:35:15.453] [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 17:35:15.456] [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 17:35:15.937] [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 17:35:15.983] [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 17:35:17.047] [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 17:35:17.180] [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 17:35:17.440] [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 17:35:17.975] [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 17:35:18.230] [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 17:35:19.185] [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 17:35:19.229] [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 17:35:19.246] [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 17:35:19.354] [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 17:35:19.354] [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 17:35:19.354] [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 17:35:19.354] [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 17:35:21.290] [puff::index::jointLog] [warning] Removed 2237 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 17:35:21.290] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 17:35:21.309] [puff::index::jointLog] [info] Replaced 740 non-ATCG nucleotides
[2021-04-08 17:35:21.309] [puff::index::jointLog] [info] Clipped poly-A tails from 645 transcripts
[2021-04-08 17:35:23.851] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 17:35:26.686] [puff::index::jointLog] [info] ntHll estimated 143845377 distinct k-mers, setting filter size to 2^32
[2021-04-08 17:36:57.296] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 17:36:57.296] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/salmon_partial_sa_index/default
[2021-04-08 17:36:57.603] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 17:36:57.612] [puff::index::jointLog] [info] contig count for validation: 1219946
[2021-04-08 17:36:58.060] [puff::index::jointLog] [info] Total # of Contigs : 1219946
[2021-04-08 17:36:58.060] [puff::index::jointLog] [info] Total # of numerical Contigs : 1219946
[2021-04-08 17:36:58.114] [puff::index::jointLog] [info] Total # of contig vec entries: 6823136
[2021-04-08 17:36:58.114] [puff::index::jointLog] [info] bits per offset entry 23
[2021-04-08 17:36:58.400] [puff::index::jointLog] [info] Done constructing the contig vector. 1219947
[2021-04-08 17:36:59.138] [puff::index::jointLog] [info] # segments = 1219946
[2021-04-08 17:36:59.138] [puff::index::jointLog] [info] total length = 181089978
[2021-04-08 17:36:59.185] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 17:37:00.518] [puff::index::jointLog] [info] positional integer width = 28
[2021-04-08 17:37:00.518] [puff::index::jointLog] [info] seqSize = 181089978
[2021-04-08 17:37:00.518] [puff::index::jointLog] [info] rankSize = 181089978
[2021-04-08 17:37:00.518] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 17:37:00.518] [puff::index::jointLog] [info] num keys = 144491598
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] mphf size = 90.2528 MB
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk size = 22636248
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 0 = [0, 22636248)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 1 = [22636248, 45272496)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 2 = [45272496, 67908744)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 3 = [67908744, 90544992)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 4 = [90544992, 113181240)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 5 = [113181240, 135817488)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 6 = [135817488, 158453736)
[2021-04-08 17:37:05.932] [puff::index::jointLog] [info] chunk 7 = [158453736, 181089948)
[2021-04-08 17:37:12.315] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 17:37:12.315] [puff::index::jointLog] [info] writing index components
[2021-04-08 17:37:14.635] [puff::index::jointLog] [info] finished writing dense pufferfish index