[mashmap] MashMap v3.1.3
[mashmap] Reference = [../../reference/hs1.fa.gz]
[mashmap] Query = [hifiasm/asm.bp.fa]
[mashmap] Kmer size = 19
[mashmap] Sketch size = 20
[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 = 24502045
[mashmap::skch::Sketch::index] unique minmers = 10660334
[mashmap::skch::Sketch::computeFreqHist] Frequency histogram of minmer interval points = (2, 7122465) ... (340212, 1)
[mashmap::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minmers occurring >= 7968 times during lookup.
[mashmap::map] time spent computing the reference index: 52.5609 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  0.52% @ 1.58e+07 bp/s elapsed: 00:00:00:01 remain: 00:00:03:12
[mashmap::skch::Map::mapQuery] mapped  0.98% @ 2.00e+07 bp/s elapsed: 00:00:00:01 remain: 00:00:02:31
[mashmap::skch::Map::mapQuery] mapped  3.82% @ 5.83e+07 bp/s elapsed: 00:00:00:02 remain: 00:00:00:50
[mashmap::skch::Map::mapQuery] mapped  8.79% @ 1.07e+08 bp/s elapsed: 00:00:00:02 remain: 00:00:00:25
[mashmap::skch::Map::mapQuery] mapped 10.57% @ 1.08e+08 bp/s elapsed: 00:00:00:03 remain: 00:00:00:25
[mashmap::skch::Map::mapQuery] mapped 17.65% @ 1.54e+08 bp/s elapsed: 00:00:00:03 remain: 00:00:00:16
[mashmap::skch::Map::mapQuery] mapped 31.26% @ 2.38e+08 bp/s elapsed: 00:00:00:04 remain: 00:00:00:08
[mashmap::skch::Map::mapQuery] mapped 42.49% @ 2.87e+08 bp/s elapsed: 00:00:00:04 remain: 00:00:00:06
[mashmap::skch::Map::mapQuery] mapped 53.12% @ 3.23e+08 bp/s elapsed: 00:00:00:05 remain: 00:00:00:04
[mashmap::skch::Map::mapQuery] mapped 60.59% @ 3.35e+08 bp/s elapsed: 00:00:00:05 remain: 00:00:00:03
[mashmap::skch::Map::mapQuery] mapped 68.45% @ 3.47e+08 bp/s elapsed: 00:00:00:06 remain: 00:00:00:02
[mashmap::skch::Map::mapQuery] mapped 83.58% @ 3.91e+08 bp/s elapsed: 00:00:00:06 remain: 00:00:00:01
[mashmap::skch::Map::mapQuery] mapped 88.45% @ 3.84e+08 bp/s elapsed: 00:00:00:07 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 90.79% @ 3.68e+08 bp/s elapsed: 00:00:00:07 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 97.67% @ 3.71e+08 bp/s elapsed: 00:00:00:08 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] mapped 100.00% @ 3.58e+08 bp/s elapsed: 00:00:00:08 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] count of mapped reads = 701, reads qualified for mapping = 705, total input reads = 705, total input bp = 3053981793
[mashmap::map] time spent mapping the query: 1.38e+01 sec
[mashmap::map] mapping results saved in: test1.mashmap