AndreaGuarracino
commented
1 year ago @ld9866, you have an old version of wfmash installed. You can solve that by changing a bit the command line
wfmash scerevisiae7.fasta.gz scerevisiae7.fasta.gz -p 90 -n 6 -t 4 -m > scerevisiae7.mapping.paf
or by updating wfmash (recommended).
When we tested the software, we found that the tutorial generated an empty file. We don't understand why. We hope you can help us to see why. Thank you！
Code: “wfmash scerevisiae7.fasta.gz -p 90 -n 6 -t 4 -m > scerevisiae7.mapping.paf” Result: [wfmash::map] Reference = [scerevisiae7.fasta.gz] [wfmash::map] Query = [] [wfmash::map] Kmer size = 15 [wfmash::map] Window size = 13 [wfmash::map] Segment length = 5000 (read split allowed) [wfmash::map] Block length min = 15000 [wfmash::map] Alphabet = DNA [wfmash::map] Percentage identity threshold = 90% [wfmash::map] Mapping output file = /dev/stdout [wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none) [wfmash::map] Execution threads = 4 [wfmash::skch::Sketch::build] minimizers picked from reference = 12004928 [wfmash::skch::Sketch::index] unique minimizers = 2043248 [wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 258463) ... (1207, 1) [wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 563 times during lookup. [wfmash::map] time spent computing the reference index: 2.96898 sec [wfmash::skch::Map::mapQuery] mapped -nan% @ 0.00e+00 bp/s elapsed: 00:00:00:00 remain: -2147483648:-3:-14:-8 [wfmash::skch::Map::mapQuery] count of mapped reads = 0, reads qualified for mapping = 0, total input reads = 0, total input bp = 0 [wfmash::map] time spent mapping the query: 5.98e-04 sec [wfmash::map] mapping results saved in: /dev/stdout