DininduSenanayake
commented
1 year ago $ module load minimap2/2.24-GCC-11.3.0
$ minimap2 --cs test/MT-human.fa test/MT-orang.fa | paftools.js stat -
[M::mm_idx_gen::0.003*2.51] collected minimizers
[M::mm_idx_gen::0.005*2.62] sorted minimizers
[M::main::0.005*2.61] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.006*2.50] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.006*2.38] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569
[M::worker_pipeline::0.025*1.35] mapped 1 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 --cs test/MT-human.fa test/MT-orang.fa
[M::main] Real time: 0.027 sec; CPU: 0.035 sec; Peak RSS: 0.004 GB
WARNING: no CIGAR at line 1
Number of mapped sequences: 0
Number of primary alignments: 0
Number of secondary alignments: 0
Number of primary alignments with >65535 CIGAR operations: 0
Number of bases in mapped sequences: 0
Number of mapped bases: 0
Number of substitutions: 0
Number of insertions in [0,50): 0
Number of insertions in [50,100): 0
Number of insertions in [100,300): 0
Number of insertions in [300,400): 0
Number of insertions in [400,1000): 0
Number of insertions in [1000,inf): 0
Number of deletions in [0,50): 0
Number of deletions in [50,100): 0
Number of deletions in [100,300): 0
Number of deletions in [300,400): 0
Number of deletions in [400,1000): 0
Number of deletions in [1000,inf): 0$ minimap2 --cs test/MT-human.fa test/MT-orang.fa | paftools.js view - | head
[M::mm_idx_gen::0.004*2.10] collected minimizers
[M::mm_idx_gen::0.006*2.37] sorted minimizers
[M::main::0.006*2.35] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.007*2.24] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.007*2.17] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569
[M::worker_pipeline::0.023*1.38] mapped 1 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 --cs test/MT-human.fa test/MT-orang.fa
[M::main] Real time: 0.025 sec; CPU: 0.033 sec; Peak RSS: 0.004 GB
>MT_orang 16499 0 16025 + MT_human 16569 576 16569 13773 16095 60 NM:i:2322 ms:i:18279 AS:i:18198 nn:i:0 tp:A:P cm:i:342 s1:i:3187 s2:i:0 de:f:0.1405 rl:i:0 mm:i:2150 oi:i:51 ei:i:102 od:i:50 ed:i:70
Ref+: 577 ==============cc=c==---=========a============t=a=======t====t=a================= 653
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Qry+: 1 ==============--=t==atc=========g============c=c=======c====-=g================= 77
Ref+: 654 ===============================a==a=====================tt========t==a=====t==a= 733
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Qry+: 78 ===============================g==g=====================cc========-==g=====c==g= 156
Ref+: 734 ===cac==tc==a====a=================g==at=========a=====t=======================a 813
minimap2 with k8