Taxonomic classifications by bacterial 10 single copy core genes
@V350057700L1C001R00600001549/1
AAAACCCCCACGATCTCAACGCCACGTTCGACTGGCTCCGCCAAGGCCGGGGGCTTTGGGAAATCTTCTTATATGCCGTGCTCGTAGGGCTGGTCTTCGAGACGTTCCTGTCCAATTGGTTCAGCCCGAAAGACACGGCGGCATAAACAGTTGCCCGGTCGTGCCCTTTTTTCCGGTTAAACAAGCGGACCGTTTTATTT
+
FFFFFFFFFBGBFFGGGFFGGFGFGFEFGFFGEGFFGGGFFGFFFFFGGFDFFGFFAFFFFFFFFGFFGFFFFFGGFFFFGFFFFFGGFFCGEFGGFFAFE4GFFFGFFFEGGGFFEF=CFE7FGFFFBFFFCF@EFF<FF5FCFFFGFEBGEFFGFFFFFEGFF)EEAFFGGGCFFFEFFGFFFFF;@DGFBCFF::FC
@V350057700L1C001R00600001562/1
TGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTGTTTGTTTGTTTGTTTGTTTGTTTTTGTGTGTTTGTGTGTTTGTTTGTTTGTTTTTTTGTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTATTTGTTTTTTTTTTTTTTTTTGTTTTTTTTTGTTTGTTTTTT
+
FF<DGEEFGFEFEFFE?GFFEF9FFG@FFFCFFGGAC<FFFGFFFGFG?G68FFFFF?FDA?GEGFF8EFEDFDFGFEE=FBBEFFFEFEAFF8GGGF>FFEEGEFBDDGDF=9FEEGGDEF7E@FGEDFGF>F@FFFFFBFGD>EFFFFFG6FGFAFFFGF7GEAGDBFEFFFGG3EEFE5G>FFEG8=CF=EFFB+DG
@V350057700L1C001R00600001768/1
TGGTGGGGCAGCGATGCAGAGGGCGTATAGTGCCAGCCGGCACCTTGTTTGTTGCGACCCGTGACAAGGTACGCTCCCACTTCTTCGGCAATCTCCGGGCTCGACGCATGGTGCTTACCGGTGCGCCGACCCCTAACAAAAGTCTCTACTAGGCTCTCTTCACTACCCGGGCCAGTCATGACAAGGACCTTTCAAGGGTG
@V350057700L1C001R00600001074/1
CGTTCAACGAGAGAATTGTCCGCCAGTTTCATGAGTCGATAGCTCGGCGGCGACAAGAGCTTCAGGCAAATCAAGAATTCACGGAAGCATTCGATGTTCCTCAACATGTTGCCGAGGTGACGCCGACGCCGCCCGCTCCTGCACCTAGACGTCGAAGAGCCGCAGTGCCCTTGAAGAAACCGTGCGTCTTTATCTGTCAC
+
GGFFGFGGFFFEGFFGFFGFGFGGGGDFFGGGGCGFGFFFFGGFFFFFFCFGBFFFGCFGGFFFGFGFFFFGGFFFFFFFEGFE6FGGFGFFGEFFFGGGFGFFGFGF:FFFFE3FF&F;FFFGF/GGGGGFGGFGFGGFGGCFGEFFBFCFGDFFF7FFFE;FCFEFGGFFF@BG=FFGFF(EF:BFFGEFGGFG@GFG
@V350057700L1C001R00600001100/1
GTCGCGGCCTGCTGCTGGCCGATACGGTGCTGGCGGAGTTGCCTTAGCCTGTCTGACGCCCCAGAACCCTCCCTCCGCGGCACTCGTAAGCAGGTTCCGATGCGTGACACAGTCCTGGTCGTACCCTGCTACAACGAAGCCGACCGTCTCGACGTCGATGCATACCTGGCGTACGCGGCCGCCGCCCCGGGCCTGCGGTT
+
BFEFFFFEFFFFFFFFFFFFFBFEFFEEFFF@FFCFBFDEFF)FFCDFFFFFFFF=FFFEFF9F,FFEFFFFFFGGFFFAFFFFGFF:FFFEFFFFFEEDFFFFAF:GFFFFCGFBFCEFFFFFEFEBFFFAFFFE+FFBF@&DFFFFFF0>==<FDAFFFFFFFFFF1BFA1DEF@FBFD/FF<EFF?>FEFF:;-:F5
@V350057700L1C001R00600001113/1
TCTACGAAGAACTTTCCCGAATACTAGGTGAAGAAACTGAGTTTAAATTTCCACAAGACAAAACAAGTATCATACTTCTTGCAGGTATACAAGGCAGCGGAAAAACAACTGTAACAGCAAAATTGGCACGTAAATTGTCTAAACAAGGTTATAGTGTTGGTGTTGTTGCTGCAGACACCTTTAGACCCGGAGCATTAGTA
metagenome~Taxonomic-classifications-by-10core-genes -c 8 -m 32 input_1/
id aneid9_1_100k aneid10_1_100k
Bacteria;Terrabacteria group;Chloroflexi 1918 476
Bacteria;PVC group;Planctomycetota;Candidatus Brocadiia;Candidatus Brocadiales;Candidatus Scalinduaceae;Candidatus Scalindua;Candidatus Scalindua sediminis 822 1310
Bacteria;Proteobacteria 822 1190
Bacteria;PVC group;Planctomycetota;Planctomycetota bacterium 822 476
Bacteria;Bacteria incertae sedis;Bacteria candidate phyla;Candidatus Aminicenantes 274 714
Bacteria;FCB group;Gemmatimonadetes 685 238
Bacteria 411 357
Bacteria;Acidobacteria 411 357
Bacteria;Terrabacteria group;Chloroflexi;Dehalococcoidia;Dehalococcoidales 274 476
pp metagenome~Taxonomic-classifications-by-10core-genes -c 8 -m 32 input_1/
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fq
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
++ docker pull c2997108/biocontainers:blast-2.13.0_core10_2
blast-2.13.0_core10_2: Pulling from c2997108/biocontainers
c1f8807f9236: Already exists
a3ed95caeb02: Already exists
f6cfdc68f728: Pulling fs layer
1581e8820cf0: Pulling fs layer
15c5b5370151: Pulling fs layer
15c5b5370151: Verifying Checksum
15c5b5370151: Download complete
f6cfdc68f728: Verifying Checksum
f6cfdc68f728: Download complete
f6cfdc68f728: Pull complete
1581e8820cf0: Download complete
1581e8820cf0: Pull complete
15c5b5370151: Pull complete
Digest: sha256:abc773a0cf6e8b30b206dec57baf92a2260149b9a71a268a12395477b3d9b4ba
Status: Downloaded newer image for c2997108/biocontainers:blast-2.13.0_core10_2
docker.io/c2997108/biocontainers:blast-2.13.0_core10_2
++ set +ex
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_1.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_2.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
##convert fastq to fasta
+ echo '##convert fastq to fasta'
+ j=input_1//alna4-02_1k_1.fasta
+ cat input_1//alna4-02_1k_1.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//alna4-02_1k_1.fasta -outfmt 6 -out input_1//alna4-02_1k_1.fasta.core10.blast -num_threads 8
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_1.fasta
+ echo '##filtering'
##filtering
+ sort
+ uniq -c
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_1.fasta.core10.blast
+ sort -nr
+ awk '{print $2"\t"$1}'
+ echo '##convert fastq to fasta'
+ j=input_1//alna4-02_1k_2.fasta
##convert fastq to 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/db/all.uscg10.fa -query input_1//alna4-02_1k_2.fasta -outfmt 6 -out input_1//alna4-02_1k_2.fasta.core10.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_2.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_2.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ awk '-F\t' '{print FILENAME"\t"$0}' '*.fasta.core10.blast'
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
+ sed s/.fasta.core10.blast//g
++ ls '*.fasta.core10.blast'
++ sort -V
awk: 致命的: ls: *.fasta.core10.blast にアクセスできません: そのようなファイルやディレクトリはありません
ファイル `*.fasta.core10.blast' を読み込み用に開けません (そのようなファイルやディレクトリはありません)
++ onerror 71
++ status=2
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
++ line=71
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes [Line 71]: Status 2
PID: 360084
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
------------------------------------------------------------
PID: 360082
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fasta.core10.blast.cnt
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fasta.core10.blast.cnt
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_1.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_2.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//alna4-02_1k_1.fasta
+ cat input_1//alna4-02_1k_1.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//alna4-02_1k_1.fasta -outfmt 6 -out input_1//alna4-02_1k_1.fasta.core10.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_1.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_1.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=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/db/all.uscg10.fa -query input_1//alna4-02_1k_2.fasta -outfmt 6 -out input_1//alna4-02_1k_2.fasta.core10.blast -num_threads 8
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_2.fasta
##filtering
+ echo '##filtering'
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_2.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ awk '-F\t' '{print FILENAME"\t"$0}' alna4-02_1k_1.fasta.core10.blast alna4-02_1k_2.fasta.core10.blast
+ sed s/.fasta.core10.blast//g
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ sort -V
++ ls alna4-02_1k_1.fasta.core10.blast alna4-02_1k_2.fasta.core10.blast
+ cd ..
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){$i=int($i*tot/cnt[i]+0.5)}; print $0}}
' /dev/fd/63 all.txt
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
++ tail -n+2 all.txt
awk: コマンドライン:3: (FILENAME=all.txt FNR=2) 致命的: ゼロによる除算が試みられました
++ onerror 77
++ status=2
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
++ line=77
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes [Line 77]: Status 2
PID: 364654
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
------------------------------------------------------------
PID: 364652
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_1.fasta.core10.blast.cnt
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/alna4-02_1k_2.fasta.core10.blast.cnt
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_1.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//alna4-02_1k_2.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//alna4-02_1k_1.fasta
+ cat input_1//alna4-02_1k_1.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//alna4-02_1k_1.fasta -outfmt 6 -out input_1//alna4-02_1k_1.fasta.core10.blast -num_threads 8
##blast
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_1.fasta
+ echo '##filtering'
##filtering
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_1.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=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/db/all.uscg10.fa -query input_1//alna4-02_1k_2.fasta -outfmt 6 -out input_1//alna4-02_1k_2.fasta.core10.blast -num_threads 8
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//alna4-02_1k_2.fasta
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//alna4-02_1k_2.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ awk '-F\t' '{print FILENAME"\t"$0}' alna4-02_1k_1.fasta.core10.blast alna4-02_1k_2.fasta.core10.blast
+ sed s/.fasta.core10.blast//g
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ sort -V
++ ls alna4-02_1k_1.fasta.core10.blast alna4-02_1k_2.fasta.core10.blast
+ cd ..
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){if(cnt[i]==0){$i=0}else{$i=int($i*tot/cnt[i]+0.5)}}; print $0}}
' /dev/fd/63 all.txt
++ tail -n+2 all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_210338_440_31752
+ echo pp20221202_210338_440_31752
+ docker run --name pp20221202_210338_440_31752 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'BEGIN{b["id"]="tax path"} FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME==ARGV[3]{print $0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt all.norm.sort.txt
+ awk '-F\t' '
{if(FNR==1){h=$0}else{for(i=2;i1{gsub(";","\t",$1); for(i=2;i<=NF;i++){if($i!=0){print $i"\t"$1 > name[i]".cnt"}}}' ../all.norm.sort.ann.sum.txt
++ sort -V
++ ls '*.cnt'
ls: *.cnt にアクセスできません: そのようなファイルやディレクトリはありません
+ ktImportText -o core10abs.html
_______________________________
____________________________________________/ KronaTools 2.7 - ktImportText \___
Creates a Krona chart from text files listing quantities and lineages.
_______
____________________________________________________________________/ Usage \___
ktImportText \
[options] \
text_1[,name_1] \
[text_2[,name_2]] \
...
text Tab-delimited text file. Each line should be a number followed by a
list of wedges to contribute to (starting from the highest level). If
no wedges are listed (and just a quantity is given), it will
contribute to the top level. If the same lineage is listed more than
once, the values will be added. Quantities can be omitted if -q is
specified. Lines beginning with "#" will be ignored. By default,
separate datasets will be created for each input (see [-c]).
name A name to show in the list of datasets in the Krona chart (if
multiple input files are present and [-c] is not specified). By
default, the basename of the file will be used.
_________
__________________________________________________________________/ Options \___
[-o ] Output file name. [Default: 'core10abs.html']
[-n ] Name of the highest level. [Default: 'all']
[-q] Files do not have a field for quantity.
[-c] Combine data from each file, rather than creating separate
datasets within the chart.
[-u ] URL of Krona resources to use instead of bundling them with
the chart (e.g. "http://krona.sourceforge.net"). Reduces size
of charts and allows updates, though charts will not work
without access to this URL.
+ mv core10abs.html ..
mv: `core10abs.html' を stat できません: そのようなファイルやディレクトリはありません
++ onerror 94
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
++ line=94
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes [Line 94]: Status 1
PID: 365539
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/krona_input
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
------------------------------------------------------------
PID: 365537
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fq
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid10_1_100k.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid9_1_100k.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//aneid10_1_100k.fasta
+ cat input_1//aneid10_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid10_1_100k.fasta -outfmt 6 -out input_1//aneid10_1_100k.fasta.core10.blast -num_threads 8
##blast
+ echo 'blast status: ' 0
+ rm input_1//aneid10_1_100k.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid10_1_100k.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//aneid9_1_100k.fasta
+ cat input_1//aneid9_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid9_1_100k.fasta -outfmt 6 -out input_1//aneid9_1_100k.fasta.core10.blast -num_threads 8
##blast
+ echo 'blast status: ' 0
+ rm input_1//aneid9_1_100k.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid9_1_100k.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ sed s/.fasta.core10.blast//g
+ awk '-F\t' '{print FILENAME"\t"$0}' aneid10_1_100k.fasta.core10.blast aneid9_1_100k.fasta.core10.blast
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ sort -V
++ ls aneid10_1_100k.fasta.core10.blast aneid9_1_100k.fasta.core10.blast
+ cd ..
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){if(cnt[i]==0){$i=0}else{$i=int($i*tot/cnt[i]+0.5)}}; print $0}}
' /dev/fd/63 all.txt
++ tail -n+2 all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_210807_545_32304
+ echo pp20221202_210807_545_32304
+ docker run --name pp20221202_210807_545_32304 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'BEGIN{b["id"]="tax path"} FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME==ARGV[3]{print $0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt all.norm.sort.txt
+ awk '-F\t' '
{if(FNR==1){h=$0}else{for(i=2;i>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid10_1_100k.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid9_1_100k.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//aneid10_1_100k.fasta
+ cat input_1//aneid10_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid10_1_100k.fasta -outfmt 6 -out input_1//aneid10_1_100k.fasta.core10.blast -num_threads 8
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//aneid10_1_100k.fasta
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid10_1_100k.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
##convert fastq to fasta
+ echo '##convert fastq to fasta'
+ j=input_1//aneid9_1_100k.fasta
+ cat input_1//aneid9_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid9_1_100k.fasta -outfmt 6 -out input_1//aneid9_1_100k.fasta.core10.blast -num_threads 8
##blast
+ echo 'blast status: ' 0
+ rm input_1//aneid9_1_100k.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid9_1_100k.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ awk '-F\t' '{print FILENAME"\t"$0}' aneid10_1_100k.fasta.core10.blast aneid9_1_100k.fasta.core10.blast
+ sed s/.fasta.core10.blast//g
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ sort -V
++ ls aneid10_1_100k.fasta.core10.blast aneid9_1_100k.fasta.core10.blast
+ cd ..
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){if(cnt[i]==0){$i=0}else{$i=int($i*tot/cnt[i]+0.5)}}; print $0}}
' /dev/fd/63 all.txt
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
++ tail -n+2 all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_211035_936_26761
+ echo pp20221202_211035_936_26761
+ docker run --name pp20221202_211035_936_26761 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'BEGIN{b["id"]="tax path"} FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME==ARGV[3]{print $0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt all.norm.sort.txt
+ awk '-F\t' '
{if(FNR==1){h=$0}else{for(i=2;i1{gsub(";","\t",$1); for(i=2;i<=NF;i++){if($i!=0){print $i"\t"$1 > name[i]".cnt"}}}' ../all.norm.sort.ann.sum.txt
++ sort -V
++ ls '*.cnt'
ls: *.cnt にアクセスできません: そのようなファイルやディレクトリはありません
+ ktImportText -o core10abs.html
_______________________________
____________________________________________/ KronaTools 2.7 - ktImportText \___
Creates a Krona chart from text files listing quantities and lineages.
_______
____________________________________________________________________/ Usage \___
ktImportText \
[options] \
text_1[,name_1] \
[text_2[,name_2]] \
...
text Tab-delimited text file. Each line should be a number followed by a
list of wedges to contribute to (starting from the highest level). If
no wedges are listed (and just a quantity is given), it will
contribute to the top level. If the same lineage is listed more than
once, the values will be added. Quantities can be omitted if -q is
specified. Lines beginning with "#" will be ignored. By default,
separate datasets will be created for each input (see [-c]).
name A name to show in the list of datasets in the Krona chart (if
multiple input files are present and [-c] is not specified). By
default, the basename of the file will be used.
_________
__________________________________________________________________/ Options \___
[-o ] Output file name. [Default: 'core10abs.html']
[-n ] Name of the highest level. [Default: 'all']
[-q] Files do not have a field for quantity.
[-c] Combine data from each file, rather than creating separate
datasets within the chart.
[-u ] URL of Krona resources to use instead of bundling them with
the chart (e.g. "http://krona.sourceforge.net"). Reduces size
of charts and allows updates, though charts will not work
without access to this URL.
+ mv core10abs.html ..
mv: `core10abs.html' を stat できません: そのようなファイルやディレクトリはありません
++ onerror 94
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
++ line=94
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes [Line 94]: Status 1
PID: 367879
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/krona_input
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~Taxonomic-classifications-by-10core-genes
------------------------------------------------------------
PID: 367877
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fasta.core10.blast.cnt
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fasta.core10.blast.cnt
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid10_1_100k.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid9_1_100k.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//aneid10_1_100k.fasta
+ cat input_1//aneid10_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
##blast
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid10_1_100k.fasta -outfmt 6 -out input_1//aneid10_1_100k.fasta.core10.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//aneid10_1_100k.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid10_1_100k.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
##convert fastq to fasta
+ echo '##convert fastq to fasta'
+ j=input_1//aneid9_1_100k.fasta
+ cat input_1//aneid9_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid9_1_100k.fasta -outfmt 6 -out input_1//aneid9_1_100k.fasta.core10.blast -num_threads 8
##blast
blast status: 0
+ echo 'blast status: ' 0
+ rm input_1//aneid9_1_100k.fasta
+ echo '##filtering'
##filtering
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid9_1_100k.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ sed s/.fasta.core10.blast.cnt//g
+ awk '-F\t' '{print FILENAME"\t"$0}' aneid10_1_100k.fasta.core10.blast.cnt aneid9_1_100k.fasta.core10.blast.cnt
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ ls aneid10_1_100k.fasta.core10.blast.cnt aneid9_1_100k.fasta.core10.blast.cnt
++ sort -V
+ cd ..
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){if(cnt[i]==0){$i=0}else{$i=int($i*tot/cnt[i]+0.5)}}; print $0}}
' /dev/fd/63 all.txt
++ tail -n+2 all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_212435_355_16688
+ echo pp20221202_212435_355_16688
+ docker run --name pp20221202_212435_355_16688 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'BEGIN{b["id"]="tax path"} FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME==ARGV[3]{print $0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt all.norm.sort.txt
+ awk '-F\t' '
{if(FNR==1){h=$0}else{for(i=2;i1{gsub(";","\t",$1); for(i=2;i<=NF;i++){if($i!=0){print $i"\t"$1 > name[i]".cnt"}}}' ../all.norm.sort.ann.sum.txt
++ sort -V
++ ls aneid10_1_100k.cnt aneid9_1_100k.cnt
+ ktImportText -o core10abs.html aneid9_1_100k.cnt aneid10_1_100k.cnt
Writing core10abs.html...
+ mv core10abs.html ..
+ cd ..
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_212454_356_28190
+ echo pp20221202_212454_356_28190
+ docker run --name pp20221202_212454_356_28190 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/centos7:3-java awk '-F\t' '
FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$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.txt ./all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_212455_169_4207
+ echo pp20221202_212455_169_4207
+ docker run --name pp20221202_212455_169_4207 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.txt all.xlsx
Start converting
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_212457_068_29611
+ echo pp20221202_212457_068_29611
+ docker run --name pp20221202_212457_068_29611 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -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
+ rm -rf krona_input
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 370358
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fq
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid10_1_100k.fasta.core10.blast.cnt
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fasta.core10.blast
1 /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/input_1/aneid9_1_100k.fasta.core10.blast.cnt
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid10_1_100k.fq 100 0.9 8 ''
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 bash run.sh input_1//aneid9_1_100k.fq 100 0.9 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//aneid10_1_100k.fasta
+ cat input_1//aneid10_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid10_1_100k.fasta -outfmt 6 -out input_1//aneid10_1_100k.fasta.core10.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//aneid10_1_100k.fasta
blast status: 0
+ echo '##filtering'
##filtering
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid10_1_100k.fasta.core10.blast
+ sort
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
##convert fastq to fasta
+ echo '##convert fastq to fasta'
+ j=input_1//aneid9_1_100k.fasta
+ cat input_1//aneid9_1_100k.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/db/all.uscg10.fa -query input_1//aneid9_1_100k.fasta -outfmt 6 -out input_1//aneid9_1_100k.fasta.core10.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//aneid9_1_100k.fasta
blast status: 0
##filtering
+ echo '##filtering'
+ sort
+ awk '-F\t' -v minB=100 -v minI=0.9 '$12>minB&&$3>minI&&$1!=old{old=$1; split($2,arr,"^"); print arr[1]}' input_1//aneid9_1_100k.fasta.core10.blast
+ uniq -c
+ sort -nr
+ awk '{print $2"\t"$1}'
+ cd input_1/
+ sed s/.fasta.core10.blast.cnt//g
+ awk '-F\t' '{print FILENAME"\t"$0}' aneid10_1_100k.fasta.core10.blast.cnt aneid9_1_100k.fasta.core10.blast.cnt
+ awk '-F\t' '
FILENAME==ARGV[1]{o[NR]=$1}
FILENAME==ARGV[2]{data[$2][$1]=$3}
END{ORS=""; print "id";
for(j=1;j<=length(o);j++){print "\t"o[j]};
print "\n";
for(i in data){print i; for(j=1;j<=length(o);j++){print "\t"data[i][o[j]]+0}; print "\n"}
}' /dev/fd/63 /dev/stdin
++ sort -V
++ ls aneid10_1_100k.fasta.core10.blast.cnt aneid9_1_100k.fasta.core10.blast.cnt
+ cd ..
+ awk '-F\t' '
{if(FNR>1){for(i=2;i<=NF;i++){cnt[$1]+=$i}; data[$1]=$0}else{data[$1]=$0}}
END{print data["id"]; PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print data[i]}}
'
+ awk '-F\t' -v tot=10000 '
FILENAME==ARGV[1]{for(i=2;i<=NF;i++){cnt[i]+=$i}}
FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; print $0}else{for(i=2;i<=NF;i++){if(cnt[i]==0){$i=0}else{$i=int($i*tot/cnt[i]+0.5)}}; print $0}}
' /dev/fd/63 all.txt
++ tail -n+2 all.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_213310_868_19114
+ echo pp20221202_213310_868_19114
+ docker run --name pp20221202_213310_868_19114 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'BEGIN{b["id"]="tax path"} FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME==ARGV[3]{print $0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt all.norm.sort.txt
+ sed 's/;unclassified[^\t]*//; s/;environmental samples[^\t]*//; s/^root;cellular organisms;//'
+ awk '-F\t' '
{if(FNR==1){h=$0}else{for(i=2;i1{gsub(";","\t",$1); for(i=2;i<=NF;i++){if($i!=0){print $i"\t"$1 > name[i]".cnt"}}}' ../all.norm.sort.ann.sum.txt
++ sort -V
++ ls aneid10_1_100k.cnt aneid9_1_100k.cnt
+ ktImportText -o core10abs.html aneid9_1_100k.cnt aneid10_1_100k.cnt
Writing core10abs.html...
+ mv core10abs.html ..
+ cd ..
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_213329_956_29769
+ echo pp20221202_213329_956_29769
+ docker run --name pp20221202_213329_956_29769 -v /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes:/yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -w /yoshitake/test/metagenome~Taxonomic-classifications-by-10core-genes -u 2007:600 -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.norm.sort.ann.sum.txt all.norm.sort.ann.sum.xlsx
Start converting
+ rm -rf krona_input
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 372674