Mercurial > repos > bgruening > salmonquantmerge

view test-data/cached_locally/prebuilt_index/ref_indexing.log @ 4:85b3dc9b6830 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
author bgruening
date Mon, 13 Jul 2020 17:14:25 -0400
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[2020-07-09 14:16:39.484] [puff::index::jointLog] [info] Running fixFasta
[2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
[2020-07-09 14:16:39.491] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-07-09 14:16:39.494] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory foo
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] contig count for validation: 23
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of Contigs : 23
[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Total # of contig vec entries: 36
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] bits per offset entry 6
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Done constructing the contig vector. 24
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] # segments = 23
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] total length = 19,592
[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Reading the reference files ...
[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] positional integer width = 15
[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] seqSize = 19,592
[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] rankSize = 19,592
[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] edgeVecSize = 0
[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] num keys = 18,902
[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk size = 9,796
[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562)
[2020-07-09 14:16:39.618] [puff::index::jointLog] [info] finished populating pos vector
[2020-07-09 14:16:39.618] [puff::index::jointLog] [info] writing index components
[2020-07-09 14:16:39.619] [puff::index::jointLog] [info] finished writing dense pufferfish index