[mashmap] MashMap v3.1.3
[mashmap] Reference = [hs1_mashmap.fa]
[mashmap] Query = [hs1_mashmap.fa]
[mashmap] Kmer size = 19
[mashmap] Sketch size = 40
[mashmap] Segment length = 5000 (read split disabled)
[mashmap] No block length filtering
[mashmap] Chaining gap max = 5000
[mashmap] Mappings per segment = 1
[mashmap] Percentage identity threshold = 95%
[mashmap] Do not skip self mappings
[mashmap] Hypergeometric filter w/ delta = 0 and confidence 0.999
[mashmap] Mapping output file = test_uncompressed.mashmap
[mashmap] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[mashmap] Execution threads  = 32
[mashmap::skch::Sketch::build] minmer windows picked from reference = 49002536
[mashmap::skch::Sketch::index] unique minmers = 19972584
[mashmap::skch::Sketch::computeFreqHist] Frequency histogram of minmer interval points = (2, 13985223) ... (344332, 1)
[mashmap::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minmers occurring >= 8288 times during lookup.
[mashmap::map] time spent computing the reference index: 56.4555 sec
[mashmap::skch::Map::mapQuery] WARNING, no .fai index found for hs1_mashmap.fa, reading the file to sum sequence length (slow)

[mashmap::skch::Map::mapQuery] mapped  0.00% @ 0.00e+00 bp/s elapsed: 00:00:00:00 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped  0.00% @ 2.06e+03 bp/s elapsed: 00:00:00:08 remain: 17:11:23:21
[mashmap::skch::Map::mapQuery] mapped 15.94% @ 5.21e+07 bp/s elapsed: 00:00:00:09 remain: 00:00:00:50
[mashmap::skch::Map::mapQuery] mapped 47.93% @ 1.49e+08 bp/s elapsed: 00:00:00:10 remain: 00:00:00:10
[mashmap::skch::Map::mapQuery] mapped 87.94% @ 2.60e+08 bp/s elapsed: 00:00:00:10 remain: 00:00:00:01
[mashmap::skch::Map::mapQuery] mapped 100.00% @ 2.83e+08 bp/s elapsed: 00:00:00:11 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] count of mapped reads = 25, reads qualified for mapping = 25, total input reads = 25, total input bp = 3117292070
[mashmap::map] time spent mapping the query: 1.73e+01 sec
[mashmap::map] mapping results saved in: test_uncompressed.mashmap