[mashmap] MashMap v3.1.3
[mashmap] Reference = [../../reference/hs1.fa]
[mashmap] Query = [hifiasm/asm.bp.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 = test1.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: 58.8227 sec
[mashmap::skch::Map::mapQuery] WARNING, no .fai index found for hifiasm/asm.bp.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  0.23% @ 1.41e+07 bp/s elapsed: 00:00:00:00 remain: 00:00:03:35
[mashmap::skch::Map::mapQuery] mapped  0.54% @ 1.11e+07 bp/s elapsed: 00:00:00:01 remain: 00:00:04:34
[mashmap::skch::Map::mapQuery] mapped  0.98% @ 1.50e+07 bp/s elapsed: 00:00:00:02 remain: 00:00:03:22
[mashmap::skch::Map::mapQuery] mapped  4.50% @ 5.49e+07 bp/s elapsed: 00:00:00:02 remain: 00:00:00:53
[mashmap::skch::Map::mapQuery] mapped  9.77% @ 9.94e+07 bp/s elapsed: 00:00:00:03 remain: 00:00:00:27
[mashmap::skch::Map::mapQuery] mapped 10.57% @ 9.22e+07 bp/s elapsed: 00:00:00:03 remain: 00:00:00:29
[mashmap::skch::Map::mapQuery] mapped 17.65% @ 1.35e+08 bp/s elapsed: 00:00:00:04 remain: 00:00:00:18
[mashmap::skch::Map::mapQuery] mapped 22.29% @ 1.51e+08 bp/s elapsed: 00:00:00:04 remain: 00:00:00:15
[mashmap::skch::Map::mapQuery] mapped 31.93% @ 1.95e+08 bp/s elapsed: 00:00:00:05 remain: 00:00:00:10
[mashmap::skch::Map::mapQuery] mapped 47.56% @ 2.64e+08 bp/s elapsed: 00:00:00:05 remain: 00:00:00:06
[mashmap::skch::Map::mapQuery] mapped 55.58% @ 2.83e+08 bp/s elapsed: 00:00:00:06 remain: 00:00:00:04
[mashmap::skch::Map::mapQuery] mapped 63.13% @ 2.96e+08 bp/s elapsed: 00:00:00:06 remain: 00:00:00:03
[mashmap::skch::Map::mapQuery] mapped 70.96% @ 3.09e+08 bp/s elapsed: 00:00:00:07 remain: 00:00:00:02
[mashmap::skch::Map::mapQuery] mapped 84.89% @ 3.46e+08 bp/s elapsed: 00:00:00:07 remain: 00:00:00:01
[mashmap::skch::Map::mapQuery] mapped 89.36% @ 3.41e+08 bp/s elapsed: 00:00:00:08 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 93.42% @ 3.36e+08 bp/s elapsed: 00:00:00:08 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 97.67% @ 3.31e+08 bp/s elapsed: 00:00:00:09 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 100.00% @ 3.21e+08 bp/s elapsed: 00:00:00:09 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] count of mapped reads = 699, reads qualified for mapping = 705, total input reads = 705, total input bp = 3053981793
[mashmap::map] time spent mapping the query: 1.53e+01 sec
[mashmap::map] mapping results saved in: test1.mashmap