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view test-data/cached_locally/prebuilt_index/ref_indexing.log @ 9:ecb9ea6269ee draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit fe9dd99a14770b6c5f26e24893599acb577e304f"
author bgruening
date Wed, 24 Mar 2021 20:15:12 +0000
parents 53d74155bb52
children
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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