c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-silva c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "(_R1.*|_1)[.]f(ast|)q$"||true`'
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-silva bash run.sh input_1/alna4-02_1k_1.fq 100 0.95 8 ''
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$'
++ true
+ echo '##count reads'
##count reads
+++ cat input_1/alna4-02_1k_1.fq
+++ wc -l
++ expr 4000 / 4
+ n0=1000
+ echo '##convert fastq to fasta'
+ j=input_1/alna4-02_1k_1.fasta
##convert fastq to fasta
+ cat input_1/alna4-02_1k_1.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
++ echo input_1/alna4-02_1k_1.fq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/alna4-02_1k_1.fq
++ sed 's/_1[.]f\(ast\|\)q$/_2.f\1q/'
+ i2=input_1/alna4-02_1k_2.fq
++ echo input_1/alna4-02_1k_1.fasta
++ egrep '_1[.]fasta$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/alna4-02_1k_1.fasta
++ sed 's/_1[.]fasta$/_2.fasta/'
+ j2=input_1/alna4-02_1k_2.fasta
+ cat input_1/alna4-02_1k_2.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/silva/SILVA_132_SSU-LSU_Ref.fasta -query input_1/alna4-02_1k_1.fasta -outfmt 6 -out input_1/alna4-02_1k_1.fasta.ssu.blast -num_threads 8
+ blastn -db /usr/local/silva/SILVA_132_SSU-LSU_Ref.fasta -query input_1/alna4-02_1k_2.fasta -outfmt 6 -out input_1/alna4-02_1k_2.fasta.ssu.blast -num_threads 8
+ python run-count-paired.py input_1/alna4-02_1k_1.fasta input_1/alna4-02_1k_2.fasta input_1/alna4-02_1k_1.fasta.ssu.blast input_1/alna4-02_1k_2.fasta.ssu.blast
+ rm input_1/alna4-02_1k_1.fasta input_1/alna4-02_1k_2.fasta
+ echo '##filtering'
##filtering
+ awk '-F\t' '$3>100{if(a[$1]==1){if($3>=topbit*0.95){print $0}}else{a[$1]=1; topbit=$3; print $0}}'
+ cat input_1/alna4-02_1k_1.fasta.ssu.all.blast
##determine LCA
+ echo '##determine LCA'
+ awk '-F\t' 'FILENAME==ARGV[1]{name[$1]=$2} FILENAME==ARGV[2]{print name[$2]"\t"$0}' /usr/local/silva/SILVA_132_SSU-LSU_Ref.fasta.name input_1/alna4-02_1k_1.fasta.ssu.blast.filtered
+ awk '-F\t' '
function searchLCA(data,  i, j, res, res2, str, n, stopflag){
 for(i in data){
  if(n==0){n=split(i,res,";")}
  else{split(i,res2,";"); for(j in res){if(res[j]!=res2[j]){res[j]=""}}}
 }
 if(res[1]!=""){str=res[1]}else{str="unknown"; stopflag=1};
 for(i=2;i<=n;i++){if(stopflag==0 && res[i]!=""){str=str";"res[i]}else{stopflag=1}}
 return str;
}
{
 if($2!=old){if(old!=""){print searchLCA(data)"\t"oldstr}; delete data; data[$1]=1; old=$2; oldstr=$0}
 else{data[$1]=1}
}
END{if(length(data)>0){print searchLCA(data)"\t"oldstr}}
' input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name
+ awk '-F\t' '{cnt[$1]++} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca
+ awk '-F\t' '{print "root;"$0}' input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt
++ awk '-F\t' '{a+=$2} END{if(a==""){a=0}; print a}' input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt
+ cnt=2
++ expr 1000 - 2
+ echo -e 'No Hit\t998'
+ awk '-F\t' '
{n=split($1,arr,";"); ORS="\t"; print $2; for(i=1;i<n;i++){print arr[i]}; ORS="\n"; print arr[n]}
' input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt2
+ echo '##krona'
##krona
+ /usr/local/KronaTools-2.7/scripts/ImportText.pl input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt3 -o input_1/alna4-02_1k_1.fq.html
tput: No value for $TERM and no -T specified
Writing input_1/alna4-02_1k_1.fq.html...
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-silva /usr/local/KronaTools-2.7/scripts/ImportText.pl input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt3 -o all.html
tput: No value for $TERM and no -T specified
Writing all.html...
+ for i in '$input_1/*.fasta.ssu.blast.filtered.name.lca.cnt2'
+++ echo input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt2
+++ sed 's/.fasta.ssu.blast.filtered.name.lca.cnt2$//'
++ basename input_1/alna4-02_1k_1
+ echo -e 'id\talna4-02_1k_1'
+ cat input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt2
+ sed 's/\t\t/\t0\t/g; s/\t\t/\t0\t/g; s/\t$/\t0/'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java merge_table.pl -k input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt2.input
You must set table files.
# Usage: *.pl [-k] <table 1> <table 2> [table 3] ...
#  -h --help       Print this message.
#  -k              Key header column exists (key must be unique, and the header must be in the first table).

+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java awk '-F\t' '
 FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}}
 FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (counts per 10000)"; if(a[i]==0){a[i]=1}}; print $0}
                   else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*10000}; print "\n"}}
' all.counts.txt ./all.counts.txt
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.txt all.counts.xlsx
Start converting
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.per.10000.txt all.counts.per.10000.xlsx
Start converting
++ find input_1/
++ egrep '([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$'
+ for i in '`find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java rm -f input_1/alna4-02_1k_1.fasta.ssu.blast.filtered
+ for i in '`find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java rm -f input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca
+ for i in '`find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java rm -f input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt
+ for i in '`find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java rm -f input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt2
+ for i in '`find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`'
+ docker run -v /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm c2997108/centos7:3-java rm -f input_1/alna4-02_1k_1.fasta.ssu.blast.filtered.name.lca.cnt3
+ 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 /tmp/181:/tmp/181 -w /tmp/181 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit