c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/centos6:2-imagemagick centos:centos6 quay.io/biocontainers/minimap2:2.16--h84994c4_0 using docker ++ docker pull c2997108/centos6:2-bwa-0.7.17-r1198-dirty 2-bwa-0.7.17-r1198-dirty: Pulling from c2997108/centos6 ff50d722b382: Already exists 800bdaf9e3a2: Already exists 10b0cc6ea1cb: Already exists 357c1092d1b6: Pulling fs layer 357c1092d1b6: Verifying Checksum 357c1092d1b6: Download complete 357c1092d1b6: Pull complete Digest: sha256:069296c796c0adc5b540fa0a4c13dbbd91d5480a987c7a72a05e9270bff7be8f Status: Downloaded newer image for c2997108/centos6:2-bwa-0.7.17-r1198-dirty ++ set +ex ++ docker pull c2997108/centos6:2-imagemagick 2-imagemagick: Pulling from c2997108/centos6 ff50d722b382: Already exists 800bdaf9e3a2: Already exists 10b0cc6ea1cb: Already exists 601c96a8f3a4: Pulling fs layer 601c96a8f3a4: Verifying Checksum 601c96a8f3a4: Download complete 601c96a8f3a4: Pull complete Digest: sha256:7f73dd92c1d5118cc7d455bcd5b70b9b8c0de4fbb565f7e19ff85a9aba5d87ba Status: Downloaded newer image for c2997108/centos6:2-imagemagick ++ set +ex ++ docker pull quay.io/biocontainers/minimap2:2.16--h84994c4_0 2.16--h84994c4_0: Pulling from biocontainers/minimap2 a3ed95caeb02: Already exists b0dc45cd432d: Already exists 9466b3513669: Already exists ddd482ea7b54: Already exists 4d69f833b9d8: Already exists e7c454e5167d: Already exists e38092b005c0: Already exists a3ed95caeb02: Already exists f879b42dfe2b: Already exists 9b835cd66ec0: Pulling fs layer 9b835cd66ec0: Verifying Checksum 9b835cd66ec0: Download complete 9b835cd66ec0: Pull complete Digest: sha256:a2bae4099d82ab716dc6a9fa8d77940d8a828ce7ae6e215ced844080a7b5a569 Status: Downloaded newer image for quay.io/biocontainers/minimap2:2.16--h84994c4_0 ++ set +ex + set -o pipefail + db=input_2/final.fasta + q=input_1/final.fasta ++ basename input_1/final.fasta ++ basename input_2/final.fasta + outbase=final.fasta-final.fasta + cpu=8 + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 input_2/final.fasta input_1/final.fasta [M::mm_idx_gen::6.760*1.68] collected minimizers [M::mm_idx_gen::7.501*2.18] sorted minimizers [M::main::7.501*2.18] loaded/built the index for 5398 target sequence(s) [M::mm_mapopt_update::8.146*2.08] mid_occ = 100 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 5398 [M::mm_idx_stat::8.572*2.03] distinct minimizers: 37787929 (98.55% are singletons); average occurrences: 1.042; average spacing: 10.451 [M::worker_pipeline::16.311*3.58] mapped 5402 sequences [M::main] Version: 2.16-r922 [M::main] CMD: minimap2 -x asm20 -t 8 input_2/final.fasta input_1/final.fasta [M::main] Real time: 16.439 sec; CPU: 58.459 sec; Peak RSS: 3.304 GB + ln -s input_2/final.fasta final.fasta-final.fasta.db.fa + ln -s input_1/final.fasta final.fasta-final.fasta.q.fa + samtools faidx final.fasta-final.fasta.db.fa + samtools faidx final.fasta-final.fasta.q.fa + in=final.fasta-final.fasta.paf + fafai1=final.fasta-final.fasta.db.fa.fai + fafai2=final.fasta-final.fasta.q.fa.fai + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' ' function abs(x){if(x<0){return -x}else{return x}} function calcarea(x1, x2, y1, y2, m1, m2){return x2*y1-x1*y2+(x2*(x2+1)-x1*(x1+1))*((y2-y1)/(x2-x1)-m2/m1)/2} FILENAME==ARGV[1]{if($11>=1*1000){ if($5=="+"){aln[$1":"$6]["+"]+=abs(calcarea($3,$4,$8,$9,$2,$7)); aln[$1":"$6]["-"]+=abs(calcarea($3,$4,$7-$8,$7-$9,$2,$7))} else{aln[$1":"$6]["+"]+=abs(calcarea($3,$4,$9,$8,$2,$7)); aln[$1":"$6]["-"]+=abs(calcarea($3,$4,$7-$9,$7-$8,$2,$7))} aln3[$1":"$6]+=$11 }} FILENAME==ARGV[2]{if($11>=1*1000){if(aln[$1":"$6]["+"]<=aln[$1":"$6]["-"]){print aln3[$1":"$6]"\t+\t"$0}else{print aln3[$1":"$6]"\t-\t"$0}}} + sort -k1,1gr -k6,6g ' final.fasta-final.fasta.paf ./final.fasta-final.fasta.paf + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' ' FILENAME==ARGV[1]{a[$3][$8]+=$1; b[$8][$3]+=$1; d[$3][$8][length(d[$3][$8])]=$0} FILENAME==ARGV[2]{ if(FNR==1){ for(i in a){ k=0; PROCINFO["sorted_in"] = "@val_num_desc"; for(j in a[i]){ max1[i]=j; break; } temp_hit_pos=0; temp_bp=0; for(j in d[i][max1[i]]){ split(d[i][max1[i]][j],arr,"\t"); temp_hit_pos+=arr[11]*(arr[11]-1)/2 - arr[10]*(arr[10]-1)/2 temp_bp+=arr[11]-arr[10]; }; avg1[i]=temp_hit_pos/temp_bp; fmax1[max1[i]][i]=1; } for(i in b){ k=0; PROCINFO["sorted_in"] = "@val_num_desc"; for(j in b[i]){ max2[i]=j; break; } temp_hit_pos=0; temp_bp=0; for(j in d[max2[i]][i]){ split(d[max2[i]][i][j],arr,"\t"); temp_hit_pos+=arr[6]*(arr[6]-1)/2 - arr[5]*(arr[5]-1)/2 temp_bp+=arr[6]-arr[5]; }; avg2[i]=temp_hit_pos/temp_bp; fmax2[max2[i]][i]=1; } }; if(check1[$3]=="" && check2[$8]==""){ check1[$3]="+"; check2[$8]=$2; delete(dafter); delete(dbefore); delete(eafter); delete(ebefore); if($3 in fmax2){ for(m in fmax2[$3]){ if(max2[m]==$3 && check2[m]==""){ split(d[max2[m]][m][0] ,arr,"\t"); if(arr[1]>arr[9]*0.1){ check2[m]=arr[2]; if(avg2[m]<($4/2)){dbefore[m]=avg2[m]}else{dafter[m]=avg2[m]} } } } }; if($8 in fmax1){ for(m in fmax1[$8]){ if(max1[m]==$8 && check1[m]==""){ split(d[m][max1[m]][0],arr,"\t"); if(arr[1]>arr[4]*0.1){ if($2=="+"){ check1[m]=arr[2] if(avg1[m]<($9/2)){ebefore[m]=avg1[m]}else{eafter[m]=avg1[m]} }else{ if(arr[2]=="+"){check1[m]="-"}else{check1[m]="+"} if(avg1[m]>($9/2)){ebefore[m]=$9-avg1[m]}else{eafter[m]=$9-avg1[m]} }; } } } }; PROCINFO["sorted_in"] = "@val_num_asc"; for(m in dbefore){print "info: "dbefore[m]"\t"check1[$3]"\t"check2[m]"\t"d[$3][m][0]} for(m in ebefore){print "info: "ebefore[m]"\t"check1[m]"\t"check2[$8]"\t"d[m][$8][0]} print "main:\t"check1[$3]"\t"check2[$8]"\t"$0; for(m in dafter){print "info: "dafter[m]"\t"check1[$3]"\t"check2[m]"\t"d[$3][m][0]} for(m in eafter){print "info: "eafter[m]"\t"check1[m]"\t"check2[$8]"\t"d[m][$8][0]} } } ' final.fasta-final.fasta.paf.da ./final.fasta-final.fasta.paf.da + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' ' FILENAME==ARGV[1]{ if(!($6 in a)){ a[$6][1]=tota*1; a[$6][4]=$2; tota+=$7; if($2=="+"){print $6"\t"tota > "final.fasta-final.fasta.paf.xp.txt"; print ".\t"tota > "final.fasta-final.fasta.paf.xm.txt"} else{print ".\t"tota > "final.fasta-final.fasta.paf.xp.txt"; print $6"\t"tota > "final.fasta-final.fasta.paf.xm.txt"} }; if(!($11 in b)){ b[$11][1]=totb*1; b[$11][4]=$3; totb+=$12; if($3=="+"){print $11"\t"totb > "final.fasta-final.fasta.paf.yp.txt"; print ".\t"totb > "final.fasta-final.fasta.paf.ym.txt"} else{print ".\t"totb > "final.fasta-final.fasta.paf.yp.txt"; print $11"\t"totb > "final.fasta-final.fasta.paf.ym.txt"} } } FILENAME==ARGV[2]{ if(!($3 in a)){ a[$3][1]=tota*1; a[$3][4]="+"; tota+=$4; print $3"\t"tota > "final.fasta-final.fasta.paf.xp.txt"; print ".\t"tota > "final.fasta-final.fasta.paf.xm.txt" }; if(!($8 in b)){ b[$8][1]=totb*1; b[$8][4]=$2; totb+=$9; if($2=="+"){print $8"\t"totb > "final.fasta-final.fasta.paf.yp.txt"; print ".\t"totb > "final.fasta-final.fasta.paf.ym.txt"} else{print ".\t"totb > "final.fasta-final.fasta.paf.yp.txt"; print $8"\t"totb > "final.fasta-final.fasta.paf.ym.txt"} }; if(a[$3][4]=="+"){x1=a[$3][1]+$5; x2=a[$3][1]+$6}else{x1=a[$3][1]+$4-$5; x2=a[$3][1]+$4-$6}; if(b[$8][4]=="+"){ if($7=="+"){y1=b[$8][1]+$10; y2=b[$8][1]+$11} else{y1=b[$8][1]+$11; y2=b[$8][1]+$10} }else{ if($7=="+"){y1=b[$8][1]+$9-$10; y2=b[$8][1]+$9-$11} else{y1=b[$8][1]+$9-$11; y2=b[$8][1]+$9-$10} } print x1"\t"x2"\t"y1"\t"y2 } FILENAME==ARGV[4]{if($1 in a){}else{tota+=$2; print $1"\t"tota > "final.fasta-final.fasta.paf.xp.txt"}} FILENAME==ARGV[3]{if($1 in b){}else{totb+=$2; print $1"\t"totb > "final.fasta-final.fasta.paf.yp.txt"}} ' final.fasta-final.fasta.paf.da3 final.fasta-final.fasta.paf.da final.fasta-final.fasta.db.fa.fai final.fasta-final.fasta.q.fa.fai + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty R --vanilla R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > xp=read.table("final.fasta-final.fasta.paf.xp.txt") > xm=read.table("final.fasta-final.fasta.paf.xm.txt") > yp=read.table("final.fasta-final.fasta.paf.yp.txt") > ym=read.table("final.fasta-final.fasta.paf.ym.txt") > if(nrow(xp)==1){xp2=0}else{xp2=c(0,xp[1:(nrow(xp)-1),2])} > if(nrow(xm)==1){xm2=0}else{xm2=c(0,xm[1:(nrow(xm)-1),2])} > if(nrow(yp)==1){yp2=0}else{yp2=c(0,yp[1:(nrow(yp)-1),2])} > if(nrow(ym)==1){ym2=0}else{ym2=c(0,ym[1:(nrow(ym)-1),2])} > #png("final.fasta-final.fasta.paf.png",width=4000,height=4000) > #library("Cairo") > #CairoPNG("final.fasta-final.fasta.paf.png",width=4000,height=4000) > pdf("final.fasta-final.fasta.paf.pdf",width=30,height=30) > b=read.table("final.fasta-final.fasta.paf.da4") > par(mar=c(10,10,4,4)) > plot(c(0,max(xp[,2])),c(0,max(yp[,2])),col="white",xaxt="n",yaxt="n", xlab="", ylab="") > axis(1,xp[,2],lab=F) > axis(2,yp[,2],lab=F) > for(i in 1:dim(xp)[1]){abline(v=xp[i,2], col='gray', lty=2)} > abline(v=0, col='gray', lty=2) > #abline(v=max(b[,1:2]), col='gray', lty=2) > for(i in 1:dim(yp)[1]){abline(h=yp[i,2], col='gray', lty=2)} > abline(h=0, col='gray', lty=2) > #abline(h=max(b[,3:4]), col='gray', lty=2) > for(i in 1:dim(b)[1]){if((b[i,2]-b[i,1])/1.0*(b[i,4]-b[i,3])/1.0>0){par(col="red")}else{par(col="blue")}; lines(c(b[i,1],b[i,2]),c(b[i,3],b[i,4]))} > par(xpd=TRUE, col="red") > text(xp[,2]-(xp[,2]-xp2)/2,par("usr")[3]-1.5,xp[,1],adj=c(1,1),srt=45) > text(par("usr")[1]-1.5,yp[,2]-(yp[,2]-yp2)/2,yp[,1],adj=c(1,1),srt=45) > par(xpd=TRUE, col="blue") > text(xm[,2]-(xm[,2]-xm2)/2,par("usr")[3]-1.5,xm[,1],adj=c(1,1),srt=45) > text(par("usr")[1]-1.5,ym[,2]-(ym[,2]-ym2)/2,ym[,1],adj=c(1,1),srt=45) > dev.off() null device 1 > + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm c2997108/centos6:2-imagemagick convert -density 300 final.fasta-final.fasta.paf.pdf final.fasta-final.fasta.paf.png + post_processing + '[' 1 = 1 ']' + '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']' + docker run -v /data/user2/work/85:/data/user2/work/85 -w /data/user2/work/85 -u root -i --rm centos:centos6 chmod -R a=rXw . + echo 0 + exit