metagenome~MAG-annotation-by-SILVA-SSU-LSU

MAG annotation by bacterial 16S and 23S rRNA

input_1:FASTA files

input_1/ProtectedArea_bin.1.fa

>k141_560463
CTCTCCGATCGACTATGAACACAAGACGGTTGTCTCCTTCGATTCCACCGATGCTTTTCT
CAGTCAGCAAAGGATGATTGAGTATCTTCCAAGGGTCGCGTTCCAAAGTTGCAACTGCCA
ACGCTTCCTTTTTCTTTTCCTTCTTTACAGCTTTCTTTTCCGGCTTCTTCTCCACTTTCT
TCTCCTCTTTTACTTTCTCGACAACTTTGTCGGCAGGCTTGGCCTGCAATTCTTCTTTAG
CCAAACTTCTCACCTAATTGTTTGAGGGAACCCTCGCTCCACACTGCCAACCTTCCGGCC
TGTCCACCGGGAGCTAAAAGTTCCGTGTTCAGTCCTGTCACCGTACTGACATCCACTCCG
GCAACGTTCCTCGCTGCCTTGGAAATTCCCTTATCGTCGGCGACAACTATGACAAGTCCT
TTCTTCGTCCTGTACTTCCTTCCACGCATCTTTCCCTTCCCCGCTCTTACCTTCCTGGGC
TTCGCCCTCTGAACGTCCGCTTCCAGTTTCAGTGCCTTGAGTACGGTGAACAGGTCCTTG

input_1/ProtectedArea_bin.2.fa

>k141_193424
AGGCGGTAAACCAAGTCGCCATGGAGAAGGACTTGCGCCAGGCCATCGAAGGCGAAGAAT
TCGCCCTCCTCTACCAACCCATCATCGACCTGCGAACGCACCACGTAATCAGCGCCGAGG
CGTTGCTGCGCTGGCATCATCCGAAGAAAGGGATCGTGTCTCCGGATGAGTTCATGCCAG
TCGCCGAGAATTCAGGATTGATCGGTCCTATTGGTGAGTGGGTATTTCGGACCGCGCTCA
AGCAGGCAAAGGATTGGCAAAAGGCGGCGGCGCGGCCACTTGGCGTTTCGGTCAATCTAT
CCAGCCGCCAAATCAGGCATGGATTCTCAAAAGAATTGGTCACGAAGGCCCTCGACGAGG
CAGGCCTTTCGCCGGATATGTTGACCATCGAGATCACCGAAAGCCTGGTCATGGAAGACA
CCGGAAGCAGCATTGATTTGATGGAATCTTTGAAAGCTATCGGTGTTGTCCTGTCGTTGG
ACGACTTTGGAACAGGCTATTCGTCCCTGAGCTATCTAAACAAATTTCCGGTTGATCTCG

input_1/ProtectedArea_bin.3.fa

>k141_21547
GTTACTCAGGGCGCAACAAAATCGCCAGATTTCGCAGAAACCTGGCTACTCCAGCCCAAT
GCGCCGGTGAATATATTCGCGAATACGCTACTGAAGACCGCATAACCACCACTGTATCAT
GTTTAAAATAATGGCGTTACAGGCTCCTCGTGCCCGCTAATGGTGAGTTAACGGTTTCCG
TAAGTTTTTTGTCAAGAAGTTTCTAGCGAAAAGCCATCCACGCGGCGACCAGCCCCACGA
CGAAGCCCGCGAGGACCTCTCCCCAGGTATGACCAACGAATTCCTTCAGGCGAGAGGGGT
CGATGTGGTGGGTGGCGCGGAGCTCATCGACCAGTTCGTTGAGTAGTCGTGCCTGCTTGC
CGACTTCCTGGCGCAGACCCGCCGCCTCGAAGACAAAGTACATACTGATGATCAGGGTCA
CGCTGAAGATCGCCGAACTGGTGCCCGCGTAGCGCCAGACGCCGATTGTCAGTGTTGTGA
CGAGCGCTGTATGGGAACTGGGCATGCCCCCGTTGTCAAATAATCTTAACAGGTTCAGTC

input_1/ProtectedArea_bin.4.fa

>k141_21929
GCGACCACGTAGTACGGGCCGCGACCCCCAATCTTGAGGCCTCGCCGCTGTCCGATCGTA
TACAGGGGAATCCCTTCGTGCGTTCCCAGGACTTGTCCCGTTTGATCACGGATGATGCCG
GGTCGGATGGCTCCAGGATGTCGCTCTCGGAGAAGTGCCCGGTAATCTCCTTCAGGAAGG
AAACAAAGCTCCTGACTATCTGGCTTGGTCGCCACGCGAAGGCCTTTCTGCGCGGCCAAT
GCCCGCACGTCACCTTTACGCATGGTGCCGAGAGGAAAACGAATTCGCCGAAGCTGCGAC
TGGGTGAGGCCGTAGAGGAAATAGCTCTGATCCTTGTCCGGATCGATTCCGCGCTTTAGC
AGGATCCTTCCGGTGGTCTGGTCCACGCCTGTCCGTGCATAGTGTCCGGTGGCGACAAAC
TCGGCTCCCCAGGCGAGGGCCCGCCGGAGGAGAGATCCGAACTTGACCTCGCTATTGCAC
GCCGCACAGGGAAGGGGGGTGCGGCCGACAGCGTACTCCTGGCAGAAGGGGGTGATGACA

input_1/ProtectedArea_bin.5.fa

>k141_83687
CCTTCGGGCAGGTGGCGCTCGGCCGCGACGCGATGCGTGAGGGCGAGGTCGTCGACGAGG
CGGCCGTCGCCGAGGCCGTCGCTCGCCTGCGCGGCGAGATCGGTCTCCGTCGCGGCAACG
TGCGGGTCGGCATCTCCAGTCCTCGCCTCATCGTGCGTCAGGTCGAGATGCCGGAGATGA
GCGAGAGCGATCTGCGCTCTGCGCTCCAGTTCCAGGCCCAGGATCTCATTCCCATTCCCG
TCGAGGAAGCGGTCCTCGACTTCGCCATTCTCGGTCGATTCGAGAACGGCGAGGGTGAGC
CCACCATGCGGGTGCTGCTCGCCGCCGCCCAGGAGGCCACGATTCTGCGCTTGGTGCAGG
CGGTGGAGGCGGCGGGACTCGGCGTCGAGTCCGTCGATCTCGTGCCGCTCGCGCTCGTCC
GAGCGATCGGCCGACCGGTAGCCGACAACGGACCGGGTGCCGAGGGGATCGTCAGCTTCG
GCGGCGGTGTCACCGTCGTCGTCGTCCATGAGCTCGGCGTCCCCGCCTTCGTGCGCGTAC

input_1/ProtectedArea_bin.6.fa

>k141_5766
CAATATGGCGCAAGCCCGACGCGCCAGCGACGAGTGCATCTTCATGCTGCTGGGAAAGGT
AATCGAGCACGCACCCACCGGTGAGATGTTTGTCACCCCGAAGCATCGACAGACGTCCGA
CTACATCGAAGGACGATACGGTTAGAAAAGGCCTATAAACTCAAGGCTCGATGGTCGTCT
CACCCGCAGCTTTCGAGCTCGAGTCTCAATCGGCCGGGCAGGCGGCTCTGCTGACGGTCG
AAGCCCGATATACCACCCAACGCGAGCGTGTCACCGATCGTCGTCGGATCTACTTCGACA
CGTTTGACTGGCGTGTTCATCGTGCTGGAGGCGTGCTGACAGCCGCCGACAATGGTCACA
CGAGCGTTCTGCGGTGGGAGACCAAGGACGGGCATCTCCAGGACCGACTGCTGGCCGCCG
GTGATCCCGGCTTCGCTTGGCAGCTCCCCGAGGGGACCTTTCGTGACTCGCTGGCCCGCG
TGATCGAGATGCGCCGGCTGCTCCCACTCGTGCGGGTGGTGACGAGCGGCGAGATGCTTC

input_1/ProtectedArea_bin.7.fa

>k141_286306
TCGCGTTTTTGCGGATTTCTGACAATTGCGTCTATGTCATTAATTTAAAATCGCTGAAAG
TCAAAAAGGTCACCTTAGACGAGACTTTTTCAAATTTGTGCGTTGGCGGTTCAGCCCTTT
ATGCCTGGGGAGCTGGTGGCAAAATAATTTCTATTAATTTTAATGGGAATGTTCGATGGG
AGTTTGATTCAAATTTGAAGATTCGCCAGGTCTCGGTCTTGAAAAATAAAATAATCATAA
GAGGGCAGGCATTGAGAACGATTTTGCTGAATGATAAAGGAGTTCTTATTCACGAAGGAA
AAATGCGGAGTTCAGGCTCCCTCTGGAATCATTATTCCAAAGATCTTCTTGAAATCGTTC
CTGAAAAAAAAATTGTAACCTGTCGCAATTTTCAGACTGATAAAATATTATGGAAAATCA
ATGTCAATGATGAAGTTAAAGCGATTGACGCGGGAGAATTGAGCGACCGTATAGGAGTTC
TTGGAGGCGATTATTTGTATTATCATTACATTATAAATAAACCTGGCTTGGTTGATGACC

input_1/ProtectedArea_bin.8.fa

>k141_33389
CGGCACGATTGAAACCTTGCGGTTTCGGCTCGTTCAGGACCCGCACAATCGTGCAATCAA
ACCGCGCGTCAGCAGGTCATTTCGCCGTGAGTGGTTTGAGTCCATACGGCACCATAGGGA
CGTTGGCTTTATCATTCCAATGACCCGTAGCATCGCAGCGACGGTCACTGCCGCAGTGCA
GGGAAGCCCCACGTTCCGCAAGCGAGGCCACCTTATATATAGGAAATGTCAACTTGGGTC
TAACGCTAGCCGAGTCGACGCCAAGGACCATCTAACCAAGATCTTCACCTTAGGCGGGCG
CTGACCCTCCTAAATTCAACTTTAAAAATAATAAGCTGCAGATTGAACTTCATGGTAAGT
ATTAGATAAGGCCAAAATCCAAGCAAAATGACTCCTTATCTATAGCGATGACAGGTAGCG
TAAAACGGTCCTTTCCGGACCTTTATGCAAAACCCAGGCCCCCCTCTATATATAGGGTGT
CCGACGCAGCGCTCGACGAGACTGACAGCCCCAGCGCGATTAACCCACCGACAACGCCAG

input_1/ProtectedArea_bin.9.fa

>k141_6347
GCATCCTCCTCGAGTACGGCGCGGACGATGAAGAGCCGCTCCTCCCCCAGTCGACCATCA
GTATCACGAGAGAAGCCGTGGTGGAGCGTCCCGCGGCCGATCAGCGTCTGGGCCTCGCCG
TTGGAGTGGATCGCGAGAAAATCGGCATCGGGATGATCGGTGCGGGCGCCTTTGGACAGT
CGGTCCTGCTGCCGGCGATCAAGAGTGTCGGCGGCTCGACGAATGTCGCCATCGCATCGG
CGGGCGGCATGACCGCACGTCGGCTCGGAGAGCAGTACGGGTTTGCCCAGGCCAGTGCCG
ATCCCGACGAGATCATCAACCACCCCGACGTCGACGCGGTGTTCGTGCTGACGCGTCACA
ACCTACACGCCGAACTCGTTGTCAAGGCGCTGCGCGCCAACAAGAACGTCTTCACGGAAA
AGCCGCTGGCGCTCTCGGAGCAAGAAGTCGACGAAATCACGGTCGCCCGCGAACAGTCCT
CGGCCGACGTCATGGTCGGCTACAACAGGCGCTTCTCGCCACTCGTGAAGCGGATCGAGC

Command

metagenome~MAG-annotation-by-SILVA-SSU-LSU -c 8 -m 32 input_1/

Output

all.path.name

id	Common taxonomy path	Dominant taxonomy path
ProtectedArea_bin.4.fa.blastn	Bacteria;Methylomirabilota;Methylomirabilia;Methylomirabilales;Methylomirabilaceae;wb1-A12	Bacteria;Methylomirabilota;Methylomirabilia;Methylomirabilales;Methylomirabilaceae;wb1-A12;uncultured bacterium

view all outputs

Log

pp metagenome~MAG-annotation-by-SILVA-SSU-LSU -c 8 -m 32 input_1/
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_silva138.1 c2997108/centos7:3-java centos:centos6
using docker
++ docker pull c2997108/biocontainers:blast-2.13.0_silva138.1
blast-2.13.0_silva138.1: Pulling from c2997108/biocontainers
c1f8807f9236: Already exists
a3ed95caeb02: Already exists
f6cfdc68f728: Already exists
66371ba13af5: Pulling fs layer
66371ba13af5: Verifying Checksum
66371ba13af5: Download complete
66371ba13af5: Pull complete
Digest: sha256:ca24b6e5c2cf563392a82a2ed96f30411e369cb7bdab557298082f4a83206f66
Status: Downloaded newer image for c2997108/biocontainers:blast-2.13.0_silva138.1
docker.io/c2997108/biocontainers:blast-2.13.0_silva138.1
++ set +ex
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ mkdir -p output_blast
+ xargs -I '{}' -P 1 bash -c '{}'
++ grep -E '[.](fa|fasta|fsa|fna)$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.1.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.2.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.3.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.4.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.5.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.6.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.7.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.8.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.9.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ cd output_blast
/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~MAG-annotation-by-SILVA-SSU-LSU: 行 51: 予期しないトークン `;' 周辺に構文エラーがあります
PID: 207152
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_silva138.1 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ mkdir -p output_blast
+ xargs -I '{}' -P 1 bash -c '{}'
++ grep -E '[.](fa|fasta|fsa|fna)$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.1.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.2.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.3.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.4.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.5.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.6.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.7.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.8.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.9.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ cd output_blast
+ for i in '*.blastn'
+ awk '-F\t' '
 FILENAME==ARGV[1]{path[$1]=$2}
 FILENAME==ARGV[2] && $12>0.98{
  if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2};
 }
 END{for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}
' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.1.fa.blastn
awk: 致命的: ファイル `/usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name' を読み込み用に開けません (そのようなファイルやディレクトリはありません)
++ onerror 44
++ status=2
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~MAG-annotation-by-SILVA-SSU-LSU
++ line=44
++ shift
++ set +x
PID: 209373
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_silva138.1 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ mkdir -p output_blast
+ xargs -I '{}' -P 1 bash -c '{}'
++ grep -E '[.](fa|fasta|fsa|fna)$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.1.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.2.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.3.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.4.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.5.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.6.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.7.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.8.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.9.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ cd output_blast
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222142_054_16104
+ echo pp20221204_222142_054_16104
+ docker run --name pp20221204_222142_054_16104 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.1.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222144_757_7771
+ echo pp20221204_222144_757_7771
+ docker run --name pp20221204_222144_757_7771 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.2.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222147_480_29039
+ echo pp20221204_222147_480_29039
+ docker run --name pp20221204_222147_480_29039 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.3.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222150_143_20494
+ echo pp20221204_222150_143_20494
+ docker run --name pp20221204_222150_143_20494 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.4.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222152_916_22421
+ echo pp20221204_222152_916_22421
+ docker run --name pp20221204_222152_916_22421 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.5.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222155_634_4456
+ echo pp20221204_222155_634_4456
+ docker run --name pp20221204_222155_634_4456 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.6.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222158_299_26141
+ echo pp20221204_222158_299_26141
+ docker run --name pp20221204_222158_299_26141 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.7.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222201_067_11832
+ echo pp20221204_222201_067_11832
+ docker run --name pp20221204_222201_067_11832 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.8.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222203_791_7378
+ echo pp20221204_222203_791_7378
+ docker run --name pp20221204_222203_791_7378 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[i]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.9.fa.blastn
+ mv all.path ..
+ cd ..
+ awk '-F\t' '
function s(e){
   compath=""; skip=0;
   for(j=1;j<=100;j++){
    if(j>1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    for(i=nstart;i1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    delete tempnode;
    for(i=nstart;i1){
   s2(NR)
  };
  old=$1; delete data; nstart=NR
 };
 data[NR][1]=$1; data[NR][2]=$2; data[NR][3]=$3; data[NR][4]=$4
}
END{
 s2(NR+1)
}' all.path
+ echo -e 'id\tCommon taxonomy path\tDominant taxonomy path'
+ cut -f 1,4,5 all.path.txt
+ sed s/.blastn.cnt//
+ uniq
+ sort -V
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 211548
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_silva138.1 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ mkdir -p output_blast
+ xargs -I '{}' -P 1 bash -c '{}'
++ grep -E '[.](fa|fasta|fsa|fna)$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.1.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.2.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.3.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.4.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.5.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.6.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.7.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.8.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.9.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ cd output_blast
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222328_148_17814
+ echo pp20221204_222328_148_17814
+ docker run --name pp20221204_222328_148_17814 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.1.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222330_681_11269
+ echo pp20221204_222330_681_11269
+ docker run --name pp20221204_222330_681_11269 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.2.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222333_425_10708
+ echo pp20221204_222333_425_10708
+ docker run --name pp20221204_222333_425_10708 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.3.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222336_080_10460
+ echo pp20221204_222336_080_10460
+ docker run --name pp20221204_222336_080_10460 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.4.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222338_792_2265
+ echo pp20221204_222338_792_2265
+ docker run --name pp20221204_222338_792_2265 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.5.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222341_409_7546
+ echo pp20221204_222341_409_7546
+ docker run --name pp20221204_222341_409_7546 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.6.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222344_195_16041
+ echo pp20221204_222344_195_16041
+ docker run --name pp20221204_222344_195_16041 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.7.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222346_948_31096
+ echo pp20221204_222346_948_31096
+ docker run --name pp20221204_222346_948_31096 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.8.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222349_604_23508
+ echo pp20221204_222349_604_23508
+ docker run --name pp20221204_222349_604_23508 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>0.98{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.9.fa.blastn
+ mv all.path ..
+ cd ..
+ awk '-F\t' '
function s(e){
   compath=""; skip=0;
   for(j=1;j<=100;j++){
    if(j>1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    for(i=nstart;i1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    delete tempnode;
    for(i=nstart;i1){
   s2(NR)
  };
  old=$1; delete data; nstart=NR
 };
 data[NR][1]=$1; data[NR][2]=$2; data[NR][3]=$3; data[NR][4]=$4
}
END{
 s2(NR+1)
}' all.path
+ echo -e 'id\tCommon taxonomy path\tDominant taxonomy path'
+ cut -f 1,4,5 all.path.txt
+ sed s/.blastn.cnt//
+ uniq
+ sort -V
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 214741
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_silva138.1 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ mkdir -p output_blast
+ xargs -I '{}' -P 1 bash -c '{}'
++ grep -E '[.](fa|fasta|fsa|fna)$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.1.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.2.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.3.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.4.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.5.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.6.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.7.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.8.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
++ basename input_1//ProtectedArea_bin.9.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 blastn -db /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ ls input_1//ProtectedArea_bin.1.fa input_1//ProtectedArea_bin.2.fa input_1//ProtectedArea_bin.3.fa input_1//ProtectedArea_bin.4.fa input_1//ProtectedArea_bin.5.fa input_1//ProtectedArea_bin.6.fa input_1//ProtectedArea_bin.7.fa input_1//ProtectedArea_bin.8.fa input_1//ProtectedArea_bin.9.fa
+ cd output_blast
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222630_966_19857
+ echo pp20221204_222630_966_19857
+ docker run --name pp20221204_222630_966_19857 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.1.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.1.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222633_665_28505
+ echo pp20221204_222633_665_28505
+ docker run --name pp20221204_222633_665_28505 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.2.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.2.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222636_335_20654
+ echo pp20221204_222636_335_20654
+ docker run --name pp20221204_222636_335_20654 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.3.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.3.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222639_007_30350
+ echo pp20221204_222639_007_30350
+ docker run --name pp20221204_222639_007_30350 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.4.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.4.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222641_876_29861
+ echo pp20221204_222641_876_29861
+ docker run --name pp20221204_222641_876_29861 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.5.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.5.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222644_719_1648
+ echo pp20221204_222644_719_1648
+ docker run --name pp20221204_222644_719_1648 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.6.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.6.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222647_421_11123
+ echo pp20221204_222647_421_11123
+ docker run --name pp20221204_222647_421_11123 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.7.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.7.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222650_074_7966
+ echo pp20221204_222650_074_7966
+ docker run --name pp20221204_222650_074_7966 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.8.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.8.fa.blastn
+ for i in '*.blastn'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221204_222652_760_4421
+ echo pp20221204_222652_760_4421
+ docker run --name pp20221204_222652_760_4421 -v /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-SILVA-SSU-LSU/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_silva138.1 awk '-F\t' 'FILENAME==ARGV[1]{path[$1]=$2} FILENAME==ARGV[2] && $12>500{if($1!=old){if(NR>1){for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}; old=$1; olds=$12; delete d; d[FNR]=$2}else if($1==old&&$12>=olds*0.98){d[FNR]=$2}} END{for(i in d){print "ProtectedArea_bin.9.fa.blastn\t"d[i]"\t"1/length(d)"\t"path[d[i]]}}' /usr/local/db/SILVA_138.1_LSU-SSURef_NR99_tax_silva.fasta.name ProtectedArea_bin.9.fa.blastn
+ mv all.path ..
+ cd ..
+ awk '-F\t' '
function s(e){
   compath=""; skip=0;
   for(j=1;j<=100;j++){
    if(j>1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    for(i=nstart;i1){if(temppath==""){break}; if(compath==""){compath=temppath}else{compath=compath";"temppath}};
    if(skip==1){break};
    temppath="";
    delete tempnode;
    for(i=nstart;i1){
   s2(NR)
  };
  old=$1; delete data; nstart=NR
 };
 data[NR][1]=$1; data[NR][2]=$2; data[NR][3]=$3; data[NR][4]=$4
}
END{
 s2(NR+1)
}' all.path
+ echo -e 'id\tCommon taxonomy path\tDominant taxonomy path'
+ cut -f 1,4,5 all.path.txt
+ sed s/.blastn.cnt//
+ uniq
+ sort -V
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 217957