Mercurial > repos > bgruening > salmonquantmerge
diff test-data/cached_locally/prebuilt_index/ref_indexing.log @ 4:85b3dc9b6830 draft
"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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/ref_indexing.log Mon Jul 13 17:14:25 2020 -0400 @@ -0,0 +1,29 @@ +[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