Had trouble to compile mummer4
Installed mummer3.23 from its binary
this worked:
$ mummer -maxmatch -n -l 100 ratg13.fasta prC31.fasta > ratg13-prc31.mumm
hqin@ECS323GPUStation:~$ cat ratg13-prc31.mumm
> hCoV-19/bat/Yunnan/PrC31/2018|EPI_ISL_1098866|2018-08
1103 1065 140
4211 4173 158
5666 5628 104
6399 6361 103
7160 7122 113
7301 7263 107
7469 7431 122
7607 7569 119
10854 10816 142
11957 11919 233
12320 12282 131
26317 26209 115
27959 27858 109
28480 28379 101
28666 28565 110
29266 29165 124
29461 29360 155
29708 29606 111
> hCoV-19/Wuhan/WH01/2019|EPI_ISL_406798|2019-12-26
191 166 134
4291 4269 120
5728 5706 105
6734 6712 146
7160 7138 104
7739 7717 101
8159 8137 104
10484 10462 106
10854 10832 124
11522 11500 107
12320 12298 116
12608 12586 204
12813 12791 157
13325 13303 193
13621 13599 113
13735 13713 107
13918 13896 111
14263 14241 116
14485 14463 111
14626 14604 158
14845 14823 134
15001 14979 203
15373 15351 143
15595 15573 116
15811 15789 113
16132 16110 179
16342 16320 137
16723 16701 140
16903 16881 104
17152 17130 146
19093 19071 335
20938 20916 116
21908 21886 131
25840 25830 119
26038 26028 115
26154 26144 162
26317 26307 200
27117 27110 132
27742 27736 139
28151 28145 127
28480 28474 101
28585 28579 203
29500 29494 141
hqin@ECS323GPUStation:~$ mummer -maxmatch -n -l 200 ratg13.fasta ncbi-ref.fasta > ratg-ncib.mumm
# reading input file "ratg13.fasta" of length 29855
# construct suffix tree for sequence of length 29855
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer ratg13.fasta 0.01
# reading input file "ncbi-ref.fasta" of length 29903
# matching query-file "ncbi-ref.fasta"
# against subject-file "ratg13.fasta"
# COMPLETETIME mummer ratg13.fasta 0.01
# SPACE mummer ratg13.fasta 0.06
hqin@ECS323GPUStation:~$ cat ratg-ncib.mumm
> NC_045512.2
12608 12611 204
15001 15004 203
19093 19096 335
26317 26332 200
28585 28604 203
hqin@ECS323GPUStation:~$ mummer -maxmatch -n -l 200 ncbi-ref.fasta ratg13.fasta > ncbi-ratg.mumm
# reading input file "ncbi-ref.fasta" of length 29903
# construct suffix tree for sequence of length 29903
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer ncbi-ref.fasta 0.01
# reading input file "ratg13.fasta" of length 29855
# matching query-file "ratg13.fasta"
# against subject-file "ncbi-ref.fasta"
# COMPLETETIME mummer ncbi-ref.fasta 0.01
# SPACE mummer ncbi-ref.fasta 0.06
hqin@ECS323GPUStation:~$ cat ncbi-ratg.mumm
> hCoV-19/bat/Yunnan/RaTG13/2013|EPI_ISL_402131|2013-07-24
12611 12608 204
15004 15001 203
19096 19093 335
26332 26317 200
28604 28585 203
No comments:
Post a Comment