Create an abundance heatmap of MAGs with full assembly
>k141_248047_length_244676_cov_69.0040
CCCACATAAGTCCCTGGGCAATAAATCCCCAAAAGAATATATGCCCAGATTTGATGAAGAATTTAAATTC
TTCATCAAATCTGACCTAAACAACAATTATTTATCGAATTTAGAGGTGTCCTAAAAAGGGGAAGCCTACA
GAAGTATAATAATTCGCAAAGAAAGCAACAAGATATTAACATTTTAACTGTTAATTATAGTCGTTTTCAG
CTTGTTGCCAACGGTCTCGTATAACCGTCAGTTACGGGTTTATATACATTAATTTTCGGTTTAGCACTGA
CGTTAGCAATTCCGAGTGGATTCGGACGTAGTCGAATCCGCCGTAATTGCGGTTATACATTGTTGGCAAC
TGGCTTTTTCCACTTTTTATTATATTTCAATTACGTATGATGTCATCGATTTTATTTTCGCACCTTTTGC
TCCTTTAAATTTGTAAAAGTCCGAAAACGCATATTTTTTTCCGTTTTGCATTTTAATAATTCCGTTTGTT
GCTCCTTCTTTTCCGTGCGATAAGATTTGGTCGATTATCAATTCTGTCGCTTTTTCGGATTTCATTTTTT
CCAATTCTTCTCTGAACTTTTCTTTTCCCTCAATTCTTTTGCCACCAATTATATCCCAAACAATTTCATC
>k141_78950_length_141674_cov_58.1554
AAGAAAACGAAACAAAAGAAAAGACCCTTCTTCACTATGTGGTCCCTAAAATCTCGGGAT
TTTAAGGACCGATGCCATGGCCTAAATTATTTCCAAGGCTTCAATAATTCTTTACGGCCA
TGACATCTCCACCACGGAAGAAGACCGACCAAACAAAAGGCTTTGCAGACAATGTTCAAC
GGAACCGAATTAGGTACTATGAGTTATCGGTACTATGTAGTTTGACGCAACAAAGAAACG
GCCTATTTTCAATTTCGTCTTAAATCAAGTGGTTTTCACATGGGGTGTAGGTAGCCCTGT
CTTCCGCCAGGCAGGCGTCCATAGAGCATTTCACTTAAGTGAAAGCGGCCTAGCCCTTGC
TAAATCTGGCTCCTACTAGCCAAGATGCACGGCACCTTGATTATTCGGCCCTGGTCGTTT
TTTGGGCGATGCAAAAAATGAACAAACACCAACTCCGGGATAGCTAGTTCTATTTTTATC
CAATTCACACACAACTTTTGGGATTGATCCTATTGATCTACTTGATTTTACAGCTAAAGC
>k141_475629_length_165948_cov_32.3676
GCGCGCACCCGGAGCACCGGCCTCTCCGGCGCCGACGGCGCCCCCGTTGAAGTTCGCCGGGCGGTTCCACGACCGGCTGGACGCCCTGGCCGAGGCGATG
TGGGAGAACCGGCAGGCCGCGGCCGAGGTCTTCGCCGACGGCGACGAACGCGCGGCCCTGGCCGCCTGGGTGATCGAGGACCTGCGGGACTCGCGGATCG
AACGCGGCCTCTTCCGCCGGCAGCCGGCCGACGCCGACCTCGCGGTCGCGCGGTTCGTGGCCCAGGTGCGGCCGGACCTGCCTCCCGTCTACAAGGGGAG
GGAACTCCGTCTGGCCGCTCTGCGGGAGGCCGCCGAGCGGACACGGGACGCGACGCACACCCACCTCGACCTCTCCCTGGAGGTGCTGGAGGTGATGGCC
GAGTACCACTGCCAGGACGCCTCCCACCCATGCGCGGAGGCGAGCGGGTGCGACGAGTACCGGCGGCTGGCGGACACGGTGCGGTCGGCGCTGGCCGCCT
ACCACTCCGCGAGCGCTCCCTACGTGTCGTGGCTGTCCGATCCGGCCGCCGTGGGCCGCCGGATCGGGGAGGACGTCGCCCACACCCCGTTCGTCCTCGC
CGCCCTCGCCCCGCGGGCCTGGCTCGAGAACGTCCGGCGGCACCGCGTCAGCGTCCCCTCGCTGTGGCGGTCGTGCCTGCCGGAGGCGCCCCTGCCCACG
GCGCCGGTGGCGGAGCAGATCGGCCACGGGATGGTGATACCCGTGTTCGCCTCCGCCCTCCAGGCCCTGGCCGCCCGCAAGCGCGAACTCGAAGGCGAGA
GACAGCGCCTTCGGGACTACGCGAGCCGGGAGAGGGGGCAGGTCCGGGCGCAGAACACCGGCGGCTGCCTGGGGGCCGTCGCCGCGGCCGTCATCCTGGT
>k141_131294_length_161699_cov_52.3814
CCACTCCCCCCACCTTTAACCCCCCGCCACCTCACCCGACACCGCGTGAGCCAGTCCGTCCGCCACCCCGGGAGCCGTCACCTCCGGCACCCTTCTTTTC
TGTTTTTCCCTTAGAATGCCCCCGAGTAATGCCCCGTTCGCGGCGCTCGACTCCGGTTTGCGTTGGGCTTCTTGGGCTTCGAGCGGCTCCTACCACCCCA
GCCAATCTTTCTAAACTGTTGATTAAATAAGTCGCGTGGGCTGTGTGCGGCGCGCAAGTGCCCCTCTTCATGCCCCCGCCGGCGGGTGGCTCGGGTGCTG
CGGCGTGGGATCATCTCGCGCGGCGGCCTCAGGCTGAAGTGGCCTGAGCAGGTGCGAAGTGCGTCAGCCTGCCGCATTTTTTCCCGGCGCATCGCTCTAA
GTCTCCGAAAATGGAACTGGCAGAGAAGGAAAGCCCAAAATGTTCAAAGGCCTAGGCATTTCAATTGGTATCATTTGCGCCGGAATGGTGGCACTTCCCG
CGCTTATCCTGGCTGCTCTTTGATGTTGCGTGAGGCCGCAAGAACGGCCTCAGTCGTCTTGGCATAACAGGGCCCTCGGGTCGCAAGGATAAAGCTTGGA
AGCGCCGCGATGGTGGTGCGTAGTTAGCAGCGTTTGCTTTGACGGTTCAGGTTCGCACAGCCGGGTCTGAGAACGCTCTGACAGTGGCCTCGCCGTGACC
TTGAGGTTATCCAAGACAGCGGTAAGGGCACCGATCATCTGCTGCGCTCCGACTATGCTAGATAGATCAGATCATCCGCGTCGGCGCCGCATGGATGCGC
CGACGCGGTCTTGCCTCAAGCGTTGGGATTGGCGAGCGTGCCAATCGTCACGTCGAGGGTCTTTTCCGCCCCCTTGTGCAGCACCGTGACCGGCACGACA
>k141_44746_length_46847_cov_42.3000
GACAGGTAATCCGTGGCTCCGATCTTGACTGCCGCCACAGCGGTGGCAATCGCGCCGTAT
CCCGTCAGCACAACGATCCGGCTATCGGGCCGTTTTTCCCGGATCACCTCGACCACGTCG
AGCCCGTTGCCATCCTCTAGCCTCAGGTCGCACACGGCATAGGCAGGGGGGCGTGCCGTG
GCAATCGCGCGCCCGGCTGCGACCGATCCGGCGGTTTCAACCTCGAACCCGCGCTTTTCC
ATCGCCTTGGCCAAACGTTTCAGAAACGCTTCGTCATCATCGACAAGCAGAAGCGACCTG
TCTTCGCCGATATCCTGAACCTCGTCAGTCATGCCGTTCCTCCCGCTCTGCCGTCCTGAC
ACAGGTTCTAGCCCGCAGCCTGACCTCCGTCAAACAAACGCGCTATTCTAACGAGCGTCA
AGAAAACACTGAACACGATCAGCTATTTGCTCTGCGGTCGCGTCTCGACGGAAAAACTCG
ACAAAGCCATGCTCGGGCAGTGTCAGATAGGTCATCGTGGAATGGTCCACGAGATAGAAA
>k141_190687_length_19080_cov_16.0000
AATACGTACAGAATGTTATCGTAGGCATAGCGAGAGCGAAAACCGCGATCCATGGGTAAGTATCTTAGCCCTTTGAGAATATCCTCGCGAGTGAAGTCAT
TGGGCGTTGGCCAAAACATTAAATCGCCGGCTCCCAAATTAAGCCCGCTACTGTGGATCAATAAATCGCGCACGCGAAACTCTGCAGTGATCCACGGATC
GGAGGTACGAAACTCTGGCAAATGATCGATAACTCGATCATCCCAGCTCAACTTGCCCTCATCGATCAGCAGCGCCAGCGCCGCACTAGTAAAGTTTTTA
CTGACCGAGGCTATCTTAAATAAGGTATTGGCTGTGACTGGCGCTGGGAGTCCGTGTTCCTGCACCCCATAGGTATTGGCAAATACCACCTGCTGCCCTT
CCACCACGGCAATGGCAACGCCAGGTACCGCATAGCTCGCCATGACCTCGGCAACGGTTTGATCAATACGCTGCGCTAGCTGCTCAGCACTCGGTTGACT
AGCGTGGCTGGAAGCCACCGATATCAGTAAGCTGACAGCGATCAGCAAATGCATAAGCGATCGGTCTATCATAGTCATGCTACTCCATACATAAGAAGGT
TACTGCCCGGCATCCGTTAACTCGAATAACTGCCCCTGCAGCACGGCATGGGTGATACGAGCACCTTGAGCAAGAAAAAAACTCGCATTTTCATCGGGCT
GGGGCTGGGCGCTGGGCGGTCTAGCCGGATTAACAAGCACCGGCCATGGCGTCTTGACCTGCAGCAGCGCTTGGTCACCCATAAAATGGCTATAACCCTG
CTGCAGCAGCTGCTGATAGTCGCTATGCTCGAGTGATAACCCAGTGGCCGGAATAGCATAGCCATTCCCCACACGATAGCTCAGCCCTTGGCCATTGAAA
@ERR5001997.1 1 length=150
CGAAATAAGGGATGCCAATATTCAACGCGATAGCATGCGCTTTAGGCGCAATATTGAACGTATTGGAGAGATTTTGGGCTACGAACTTAGCAAGACCCTTGACTATAGGAACCAAACGGTCGAAACCCCTATGGGAACCAAAGAAATGTC
+ERR5001997.1 1 length=150
F:FFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFF,FFFFFFFFFF,F:FFFFFFFFFFF:FFFFFF:FFF,FFFF:FFFFFF:FFF:FFFFFFFFF:,FFFFFFFFFF:F:FFFFFFFF:FFFF::FF,,:F,FFFFFF:FFF:FF,FF
@ERR5001997.2 2 length=151
GTGTAATCAGTCCTCACCCTCATTAATTGAGCTGAGCTCGTCGGACCGTGCCTGCTCAACTTCGTCTGCTGATGGCCCTAAGTCTTCGATCATTGACTCCGCACGCTTGCGACGACGTTCTGCATGGTAAGTTAAACCTGTACCTGCTGGA
+ERR5001997.2 2 length=151
F:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFF:F,FFFFFF:F:FF,F:F:,FFFFFF:,FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFF,,,F,FFFF:FFFFFFFF
@ERR5001997.3 3 length=151
CAGGCAAGACCGTCTTCCGGAAGCGGATCGCGGAAAACCGGCATCGCCGGAAGCACCCGGCGCAAGGGCCCACATGCGGCAAGGACGGTCACTCCGGCGGCCATCCAGCCGGTTCGGCGCAGGAAGTCTCGCCGTCCGAGAGTCTTTGAGT
@ERR5001997.1 1 length=151
AAAAGCATCCTCATCTCCACGGTGATGCCTATATGCAGAAATAAAAGCATTTTCCGCATTGTCGAAATAGTTTAACAGGCCCTGATGTAATGGGAGTCCGGCACGTAAAACGGAGCACAGCACCAAATCATCGATAGGCATGGACATTTCT
+ERR5001997.1 1 length=151
,FFFFF::FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF,FFFFFFF:FFFFF::FFF:F:FFFF:FFF:FFFFFFFF:FF:F:FFFFFFFFFFFFFFFF,FFFFF,FFF:FFFFFFFFF
@ERR5001997.2 2 length=150
ACCAAAGCTTCATTGGCAACTGAGTCCTTTATTTCTGCGGCTTCCTTCCAGGAAACCACGCGTGTTCTTACCGAAGCAGCAGTCAATGGTAAGACCGATGATTTACGTGGCTTGAAAGAGAACGTGATCGTGGGACGTCTGATTCCAGCA
+ERR5001997.2 2 length=150
FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFF::FFF:F,FFFFFFF,FFF:FFFFF:FFFFF,FFFFFFF
@ERR5001997.3 3 length=151
CCAGGGCAGATCATGCAGGCGGCGGCTTTGTTGGAGCGCATCCCGTCGCCCTCCGATGCCGAGATCCGGGAGTGGATGAACGGGAATCTCTGCCGTTGCGGAACCTATGCACGGATCCGCGCCGCCGTCCGGCGCGCGTCCGGGACACCAT
@ERR5001999.1 1 length=149
GGGACTGGAGCTGGGTGCCGATGACTACCTGGTAAAGCCCTTCGCGTTTGCCGAGTTACTGGCGCGGGTACGCACACTGTTGCGTCGAGGATCGGCACCACCTCTGACGGATCAGCTCAGGGTGGCCAACCTTACGCTGGATTTACCCA
+ERR5001999.1 1 length=149
FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF
@ERR5001999.2 2 length=151
AGCGGTTGCCGTCGTGCGGACTAACTGATGATGAATTGAAATCAGAGGTGTTTCAAACCTTTTGTGATTTGCTTCGCTGGTACAGACCTCAAGCCAAAGATGAACGAACGCCGCAGAGCTTTCGGACTTTTTGCCGACAGTTCGGGGCAAA
+ERR5001999.2 2 length=151
FFFF,F:FFFFF,FFFFFFFFFFF:,F:,FFFFFFFF,FFFFFF:F,FF,:FFFFFF:,:FFFFFFFFF:,:,FFFF,FF:F:FFFF:FFFF,FF::FFFFFF:F::FF:FFFFF,FFF:FF,F:FFFFFFFF,FF:FF:FF,FF,F:FFF
@ERR5001999.3 3 length=150
GTAATAAAACCCACGGCGGTTGGCTGGAATCAGGCCAAGAATTGGCCGGACTGGGAGTTAATTTAATATTGGAGTACCAAACTACAGAAGTCTGGGACGACATTATATAGCGCGACGCACACACCAAATTTGACGATACATATGGTACTT
@ERR5001999.1 1 length=150
CGCCCTGGCGTCGTACCAGCAGTTCCAGCAGGCAGAACTCCTTGTGGCTGAGACTGATTTTCCGACCAGCACGCGTAACTTGATGCCTGGGTAAATCCAGCGTAAGGTTGGCCACCCTGAGCTGATCCGTCAGAGGTGGTGCCGATCCTC
+ERR5001999.1 1 length=150
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ERR5001999.2 2 length=151
GCCAGAAATCTCGGCGTTCTAATCTCGCCACGGCACTTTCAACTTTCGGAATATCCCAGAATCCGTATTGGTGGCGAACAATTCCGTTTTGCTCATCTTCTTCAATCTGCTCTTTGATTCTGTTTGCCAAATCCCTTATCCTGCGATCTTT
+ERR5001999.2 2 length=151
FF,FF:FFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:,FFFFFFFFF::FFFFFFFF,FF:,:F,FFFFFFFFFFFFFF,:FFFF:FFFFFF:FFFF:FFFFFF:FFFF,FFFFFFFFF,FFF:FFFFFF,FF:,FFFF,FFFFF
@ERR5001999.3 3 length=149
GAGAAGAATACTGCCCCTCAGGATCCAGAGCTTGGGCTAGGCCCGGGCCAGTGCACAAGTTACCGCGGTCTTGAATACCTGCGCGCAGCGTCCAATGGTTTTTACCCATTTCGAAGCTGGCATCCAATTGGTCCACGCCCGTGTTTACA
>k141_248047_length_244676_cov_69.0040
CCCACATAAGTCCCTGGGCAATAAATCCCCAAAAGAATATATGCCCAGATTTGATGAAGAATTTAAATTC
TTCATCAAATCTGACCTAAACAACAATTATTTATCGAATTTAGAGGTGTCCTAAAAAGGGGAAGCCTACA
GAAGTATAATAATTCGCAAAGAAAGCAACAAGATATTAACATTTTAACTGTTAATTATAGTCGTTTTCAG
CTTGTTGCCAACGGTCTCGTATAACCGTCAGTTACGGGTTTATATACATTAATTTTCGGTTTAGCACTGA
CGTTAGCAATTCCGAGTGGATTCGGACGTAGTCGAATCCGCCGTAATTGCGGTTATACATTGTTGGCAAC
TGGCTTTTTCCACTTTTTATTATATTTCAATTACGTATGATGTCATCGATTTTATTTTCGCACCTTTTGC
TCCTTTAAATTTGTAAAAGTCCGAAAACGCATATTTTTTTCCGTTTTGCATTTTAATAATTCCGTTTGTT
GCTCCTTCTTTTCCGTGCGATAAGATTTGGTCGATTATCAATTCTGTCGCTTTTTCGGATTTCATTTTTT
CCAATTCTTCTCTGAACTTTTCTTTTCCCTCAATTCTTTTGCCACCAATTATATCCCAAACAATTTCATC
metagenome~mapping-to-MAG-with-full-assembly input_1/ input_2/ input_3/all.fa
pp metagenome~mapping-to-MAG-with-full-assembly input_1/ input_2/ input_3/publicareaall.fa
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.1.fa
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.10.fa
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.11.fa
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.12.fa
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.13.fa
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_1/PublicArea_bin.14.fa
0 input_2/
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_2/ERR5001997_1.fastq
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_2/ERR5001997_2.fastq
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_2/ERR5001999_1.fastq
1 /yoshitake/test/metagenome~mapping-to-MAG-with-full-assembly/input_2/ERR5001999_2.fastq
0 input_3/all.fa
c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:7 centos:centos6 quay.io/biocontainers/samtools:1.9--h91753b0_3 quay.io/biocontainers/seqkit:0.12.1--0
using docker
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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> library("Cairo")
> library("gplots")
>
> a=read.table("all.txt",sep="\t",row.names=1,header=T)
>
> myh=min(10000,dim(a)[1]*12+500)
> if(myh*0.1<200){myh2=200}else{myh2=myh*0.1}
> CairoPNG(file="output.png",width=min(10000,dim(a)[2]*12+500),height=min(10000,dim(a)[1]*12+500));
> heatmap.2(as.matrix(log10(a+min(a[a>0]))),cexCol = 1, cexRow = 1, trace="none", margins=c(20,20), lhei=c(myh2, myh))
> dev.off()
null device
1
>
PID: 450555