Mercurial > repos > bgruening > alevin
view test-data/cached_locally/prebuilt_index/ref_indexing.log @ 16:b0fe3e482cb7 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 6954ddebecfe9f0975f2c7e29193e4c99c550514
| author | bgruening |
|---|---|
| date | Mon, 28 Oct 2024 17:50:35 +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