metagenome~MAG-annotation-by-10core-genes

MAG annotation by bacterial 10 single copy core genes

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-10core-genes -c 8 -m 32 input_1/

Output

all.path.name

id	Common taxonomy path	Dominant taxonomy path
ProtectedArea_bin.2.fa	Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales	Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Magnetovibrio
ProtectedArea_bin.3.fa	Bacteria;Proteobacteria;Alphaproteobacteria;Hyphomicrobiales;Hyphomicrobiaceae;Methyloceanibacter	Bacteria;Proteobacteria;Alphaproteobacteria;Hyphomicrobiales;Hyphomicrobiaceae;Methyloceanibacter
ProtectedArea_bin.4.fa	Bacteria;Bacteria incertae sedis;Bacteria candidate phyla;candidate division NC10;Candidatus Methylomirabilis	Bacteria;Bacteria incertae sedis;Bacteria candidate phyla;candidate division NC10;Candidatus Methylomirabilis
ProtectedArea_bin.5.fa	Bacteria;Terrabacteria group;Actinobacteria	Bacteria;Terrabacteria group;Actinobacteria
ProtectedArea_bin.8.fa	Bacteria	Bacteria;Proteobacteria;Gammaproteobacteria;Nitrospirales
ProtectedArea_bin.9.fa	Bacteria	Bacteria;Proteobacteria

view all outputs

Log

pp metagenome~MAG-annotation-by-10core-genes -c 8 -m 32 input_1/
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_core10_2 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 "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$input_1"/*|grep -E "[.](fa|fasta|fsa|fna)$"`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-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 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/input_1//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
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.1.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.2.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.3.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.4.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.5.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.6.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.7.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.8.fa.blastn'
Command line argument error: Argument "out". File is not accessible:  `output_blast/input_1//ProtectedArea_bin.9.fa.blastn'
++ onerror 37
++ status=123
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~MAG-annotation-by-10core-genes
++ line=37
++ shift
++ set +x

------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~MAG-annotation-by-10core-genes [Line 37]: Status 123

PID: 379734
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/metagenome~MAG-annotation-by-10core-genes
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/metagenome~MAG-annotation-by-10core-genes 
------------------------------------------------------------

PID: 379732
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_core10_2 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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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-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 blastn -db /usr/local/db/all.uscg10.fa -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'
+ cat ProtectedArea_bin.1.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.2.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.3.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.4.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.5.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.6.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.7.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.8.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.9.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.1.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.2.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.2.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.3.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.3.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.4.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.4.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.5.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.5.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.6.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.7.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.8.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.8.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.9.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.9.fa.blastn.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_223902_936_6294
+ echo pp20221202_223902_936_6294
+ sed 's/;unclassified.*//; s/;environmental samples.*//; s/root;cellular organisms;//'
+ docker run --name pp20221202_223902_936_6294 -v /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME!=ARGV[1]&&FILENAME!=ARGV[2]{print FILENAME"\t"$0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt ProtectedArea_bin.2.fa.blastn.cnt ProtectedArea_bin.3.fa.blastn.cnt ProtectedArea_bin.4.fa.blastn.cnt ProtectedArea_bin.5.fa.blastn.cnt ProtectedArea_bin.8.fa.blastn.cnt ProtectedArea_bin.9.fa.blastn.cnt
+ 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]=$4
}
END{
 s2(NR+1)
}' all.path
+ echo -e 'id\tCommon taxonomy path\tDominant taxonomy path'
+ cut -f 1,4,5 all.path.txt
+ sed s/.blastn.cnt//
+ uniq
+ sort -V
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 382659
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.1.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.2.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.3.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.4.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.5.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.6.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.7.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.8.fa
1 /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/input_1/ProtectedArea_bin.9.fa
c2997108/biocontainers:blast-2.13.0_core10_2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
++ echo input_1/
++ grep '[.]gz$'
++ 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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.1.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.1.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.2.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.2.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.3.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.3.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.4.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.4.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.5.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.5.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.6.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.6.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.7.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.7.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.8.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.8.fa.blastn
+ for i in '`ls "$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 '$PPDOCNAME' '>>' '/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 blastn -db /usr/local/db/all.uscg10.fa -query input_1//ProtectedArea_bin.9.fa -outfmt 6 -num_threads 8 -out output_blast/ProtectedArea_bin.9.fa.blastn
++ grep -E '[.](fa|fasta|fsa|fna)[.]gz$'
++ 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'
+ cat ProtectedArea_bin.1.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.2.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.3.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.4.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.5.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.6.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ awk '-F\t' '$12>90&&$3>90'
+ cat ProtectedArea_bin.7.fa.blastn
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.8.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ cat ProtectedArea_bin.9.fa.blastn
+ awk '-F\t' '$12>90&&$3>90'
+ awk '-F\t' '
 BEGIN{d[0]=0; delete d}
 {
  if($1==old){
   f=1;
   for(i=1;i<=length(d);i++){
    if(($7>=d[i][1]&&$7<=d[i][2])||($8>=d[i][1]&&$8<=d[i][2])){dupid=0; if($120){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
   delete d; d[1][0]=$0; d[1][1]=$7; d[1][2]=$8; d[1][3]=$12; old=$1
  }
 }
 END{
   if(length(d)>0){
    for(i=1;i<=length(d);i++){
     val=d[i][4]+1; if(d[i][5]!=0){val=d[d[i][5]][4]+1};
     print d[i][0]"\t"val}
   };
 }'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.1.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.2.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.2.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.3.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.3.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.4.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.4.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.5.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.5.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.6.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.7.fa.blastn.txt ']'
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.8.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.8.fa.blastn.txt
+ for i in '*.blastn'
+ '[' -s ProtectedArea_bin.9.fa.blastn.txt ']'
+ awk '-F\t' '{split($2,arr,"^"); cnt[arr[1]]+=1/$13} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' ProtectedArea_bin.9.fa.blastn.txt
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221202_224146_442_21150
+ echo pp20221202_224146_442_21150
+ sed 's/;unclassified.*//; s/;environmental samples.*//; s/root;cellular organisms;//'
+ docker run --name pp20221202_224146_442_21150 -v /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast:/yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast -w /yoshitake/test/metagenome~MAG-annotation-by-10core-genes/output_blast -u 2007:600 -i --rm c2997108/biocontainers:blast-2.13.0_core10_2 awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=$2} FILENAME==ARGV[2]{b[$1]=a[$2]} FILENAME!=ARGV[1]&&FILENAME!=ARGV[2]{print FILENAME"\t"$0"\t"b[$1]}' /usr/local/db/names.dmp.sname.path /usr/local/db/ac2tax.txt ProtectedArea_bin.2.fa.blastn.cnt ProtectedArea_bin.3.fa.blastn.cnt ProtectedArea_bin.4.fa.blastn.cnt ProtectedArea_bin.5.fa.blastn.cnt ProtectedArea_bin.8.fa.blastn.cnt ProtectedArea_bin.9.fa.blastn.cnt
+ 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: 385029