Make an alignment file for Mauve. If you finish this pipeline, you can use a mauve-align file and output_for_mauve for chromosome names. You can see chromosome names if you check "View -> Style -> Annotated features -> Always show" on Mauve.
>BK006935.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome I, complete sequence
ccacaccacacccacacacccacacaccacaccacacaccacaccacacccacacacacacatCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
TCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC
CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATAT
TGAAACGCTAACAAATGATCGTAAATAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCAC
CCTCACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC
CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGG
TCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGCGGTcccaaat
attgtataaCTGCCCTTAATACATACGTTATACCACTTTTGCACCATATACTTACCACTCCATTTATATACACTTATGTC
>CP004488.2 Saccharomyces cerevisiae YJM1447 chromosome I genomic sequence
GAAGACACTTAAACCACTACCGGCCAGTAAGCTGTTGGCACTGCCAGCATACgttgaaatttctaaagAAGCTGTACTAG
ATCCTACCATGCTGCTTACTGGTGTGCTACGAGGCTGTTGCGACATAGTACTCAACCCGGAACTTGTTAGACTCTTGGTG
TTGCCAGTTTCGGATACAGAAACAACACTACTGCTGTGACCAATCACGTCGGTCGCGGAATCCGTCTGTGTTTCAGCGTG
ATTAGATCTTGAAAGCGAAGAGGTGACTACTGTTTTCGTCTCAGCAGCTCCAGTATTGGTAGTCGTTTCAGCAGCTACAG
TATTGGTTGTTGTCTCACTGGTAGCACTGTTCATTTTAGAGCTGACAGAATCTTCATTCGTAGTCTGTGGCCTCCATGTA
GGATAGACCGTAACAACATCATTCACAGTAGCCGTGGCCGTCGAAACAATGGCAGGTGAAGCAGTTTCGGAACACACACC
AGATTCGCAGGAAGTAACAGTAACTAGCGTAGTTTGTTGCCTCGATTCTGTGGTGGAAATAGGACACCATGTTGTGTATT
CCGTGGTAACGCCGTTAATAGTAGCAGTGCTTGTAGACACAATGGCTGGAGAAGCAGTCTTGGAGCATACGTCAGATtca
caagaagaaattgtaACTACTGTGGTTTGTTTTGTTTCTGTGGTTTGCTCTGTTGTCCCTTTGGTTTGCTTTGTTGTCTC
Comparative-genomics~make-align-for-mauve -c 8 -m 32 input_1/
#FormatVersion Mauve1
#Sequence1File output_for_mauve/q.fa.gb
#Sequence1Format GenBank
#Annotation1File output_for_mauve/q.fa.gb
#Annotation1Format GenBank
#Sequence2File output_for_mauve/ref.fa.gb
#Sequence2Format GenBank
#Annotation2File output_for_mauve/ref.fa.gb
#Annotation2Format GenBank
#BackboneFile mauve-align.bbcols
pp Comparative-genomics~make-align-for-mauve -c 8 -m 32 input_1/
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7 centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve: 行 44: 予期しないトークン `xargs' 周辺に構文エラーがあります
PID: 369188
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7 centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140839_006_25685
+ echo pp20221021_140839_006_25685
+ docker run --name pp20221021_140839_006_25685 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140839_825_9243
+ echo pp20221021_140839_825_9243
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_140839_825_9243 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140840_473_3134
+ echo pp20221021_140840_473_3134
/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve: 行 58: NCPU: 未割り当ての変数です
++ onerror 64
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
++ line=64
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve [Line 64]: Status 1
PID: 369931
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/Comparative-genomics~make-align-for-mauve
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
------------------------------------------------------------
PID: 369929
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7 centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140856_783_27681
+ echo pp20221021_140856_783_27681
+ docker run --name pp20221021_140856_783_27681 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140857_521_31419
+ echo pp20221021_140857_521_31419
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_140857_521_31419 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140858_188_15474
+ echo pp20221021_140858_188_15474
+ docker run --name pp20221021_140858_188_15474 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.476*1.09] collected minimizers
[M::mm_idx_gen::0.676*1.45] sorted minimizers
[M::main::0.676*1.45] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.734*1.42] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.777*1.39] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.904*1.85] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 2.924 sec; CPU: 5.405 sec; Peak RSS: 0.241 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ sort -k1,1 -k3,3gr '-t '
+ awk 'a[$1]==0{a[$1]=1; print $0}'
++ basename reformat_fasta/q.fa
+ sort -k2,2 -k7,7n '-t '
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140901_785_7745
+ echo pp20221021_140901_785_7745
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_140901_785_7745 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7 awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140902_422_17547
+ echo pp20221021_140902_422_17547
+ docker run --name pp20221021_140902_422_17547 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_140903_206_1572
+ echo pp20221021_140903_206_1572
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_140903_206_1572 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 370926
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7 centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141058_673_26916
+ echo pp20221021_141058_673_26916
+ docker run --name pp20221021_141058_673_26916 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141059_654_18718
+ echo pp20221021_141059_654_18718
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_141059_654_18718 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141100_735_5535
+ echo pp20221021_141100_735_5535
+ docker run --name pp20221021_141100_735_5535 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.509*1.09] collected minimizers
[M::mm_idx_gen::0.711*1.40] sorted minimizers
[M::main::0.711*1.40] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.769*1.37] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.804*1.36] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.929*1.84] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 2.957 sec; CPU: 5.412 sec; Peak RSS: 0.234 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ awk 'a[$1]==0{a[$1]=1; print $0}'
+ sort -k1,1 -k3,3gr '-t '
++ basename reformat_fasta/q.fa
+ sort -k2,2 -k7,7n '-t '
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141104_388_9798
+ echo pp20221021_141104_388_9798
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_141104_388_9798 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7 awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141105_059_30169
+ echo pp20221021_141105_059_30169
+ docker run --name pp20221021_141105_059_30169 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_141106_073_32279
+ echo pp20221021_141106_073_32279
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_141106_073_32279 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 372717
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7-mauve centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
++ egrep '[.](fa|fasta|fsa|fna)$'
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142635_556_23961
+ echo pp20221021_142635_556_23961
+ docker run --name pp20221021_142635_556_23961 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142636_548_32642
+ echo pp20221021_142636_548_32642
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_142636_548_32642 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142637_724_24707
+ echo pp20221021_142637_724_24707
+ docker run --name pp20221021_142637_724_24707 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.514*1.14] collected minimizers
[M::mm_idx_gen::0.690*1.55] sorted minimizers
[M::main::0.690*1.55] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.741*1.51] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.775*1.49] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.931*1.90] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 2.958 sec; CPU: 5.610 sec; Peak RSS: 0.242 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ sort -k1,1 -k3,3gr '-t '
++ basename reformat_fasta/q.fa
+ sort -k2,2 -k7,7n '-t '
+ awk 'a[$1]==0{a[$1]=1; print $0}'
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142641_371_28636
+ echo pp20221021_142641_371_28636
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_142641_371_28636 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142641_985_28488
+ echo pp20221021_142641_985_28488
+ docker run --name pp20221021_142641_985_28488 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142643_003_31812
+ echo pp20221021_142643_003_31812
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_142643_003_31812 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
+ /usr/local/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=mauve-align --output-guide-tree=mauve-align.guide_tree --backbone-output=mauve-align.backbone output_for_mauve/q.fa.gb output_for_mauve/ref.fa.gb
/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve: 行 69: /usr/local/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve: そのようなファイルやディレクトリはありません
++ onerror 69
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
++ line=69
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve [Line 69]: Status 1
PID: 378120
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/Comparative-genomics~make-align-for-mauve
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
------------------------------------------------------------
PID: 378118
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7-mauve centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142749_538_12835
+ echo pp20221021_142749_538_12835
+ docker run --name pp20221021_142749_538_12835 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142750_675_20398
+ echo pp20221021_142750_675_20398
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_142750_675_20398 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142751_840_16211
+ echo pp20221021_142751_840_16211
+ docker run --name pp20221021_142751_840_16211 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.537*1.09] collected minimizers
[M::mm_idx_gen::0.704*1.52] sorted minimizers
[M::main::0.704*1.52] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.749*1.49] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.783*1.47] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.969*1.87] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 2.992 sec; CPU: 5.566 sec; Peak RSS: 0.246 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ awk 'a[$1]==0{a[$1]=1; print $0}'
++ basename reformat_fasta/q.fa
+ sort -k2,2 -k7,7n '-t '
+ sort -k1,1 -k3,3gr '-t '
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142755_532_8085
+ echo pp20221021_142755_532_8085
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_142755_532_8085 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142756_200_8066
+ echo pp20221021_142756_200_8066
+ docker run --name pp20221021_142756_200_8066 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142757_181_9483
+ echo pp20221021_142757_181_9483
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_142757_181_9483 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_142758_332_22025
+ echo pp20221021_142758_332_22025
+ docker run --name pp20221021_142758_332_22025 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve /usr/local/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=mauve-align --output-guide-tree=mauve-align.guide_tree --backbone-output=mauve-align.backbone output_for_mauve/q.fa.gb output_for_mauve/ref.fa.gb
Storing raw sequence at /tmp/rawseq1.000
Sequence loaded successfully.
output_for_mauve/q.fa.gb 12142016 base pairs.
Storing raw sequence at /tmp/rawseq1.001
Sequence loaded successfully.
output_for_mauve/ref.fa.gb 12071326 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
Sorted mer list loaded successfully
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
using default bp penalty: 164705
using default bp estimate min score: 494115
Starting with 69309 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.0932985
0.0932985 0
Writing guide tree to mauve-align.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 2149 initial LCBs
Using scaled bp penalty: 333953
Pair (0,1) has 4 well-supported breakpoints
genome content distance matrix:
0 0.0932985
0.0932985 0
bp distance matrix:
0.9 0.0198895
0.0198895 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68120 tracking matches
There are 136240 / 204360 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 2163 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 14 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 9.70802e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 104 new matches outside LCBs
0,0 has an additional 1813 matches
Restoring backed up alignment tree...
1,0 has 1813 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68704 tracking matches
There are 137408 / 206112 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 1081 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 13 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 9.70802e+08, new anchor score: 9.6729e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 4 superintervals
root alignment length: 13000370
Organisms have 38.4% GC
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 379996
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7-mauve centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143032_824_4511
+ echo pp20221021_143032_824_4511
+ docker run --name pp20221021_143032_824_4511 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143033_856_6308
+ echo pp20221021_143033_856_6308
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_143033_856_6308 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143034_985_14492
+ echo pp20221021_143034_985_14492
/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve: 行 62: a: 未割り当ての変数です
++ onerror 68
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
++ line=68
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve [Line 68]: Status 1
PID: 381863
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/Comparative-genomics~make-align-for-mauve
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
------------------------------------------------------------
PID: 381861
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7-mauve centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143102_891_29298
+ echo pp20221021_143102_891_29298
+ docker run --name pp20221021_143102_891_29298 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143103_843_22538
+ echo pp20221021_143103_843_22538
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_143103_843_22538 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143104_965_28933
+ echo pp20221021_143104_965_28933
+ docker run --name pp20221021_143104_965_28933 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.531*1.10] collected minimizers
[M::mm_idx_gen::0.733*1.44] sorted minimizers
[M::main::0.733*1.44] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.791*1.41] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.835*1.39] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.994*1.86] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 3.017 sec; CPU: 5.584 sec; Peak RSS: 0.241 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ awk 'a[$1]==0{a[$1]=1; print $0}'
++ basename reformat_fasta/q.fa
+ sort -k1,1 -k3,3gr '-t '
+ sort -k2,2 -k7,7n '-t '
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143108_707_15950
+ echo pp20221021_143108_707_15950
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_143108_707_15950 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143109_400_3684
+ echo pp20221021_143109_400_3684
+ docker run --name pp20221021_143109_400_3684 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143110_438_24362
+ echo pp20221021_143110_438_24362
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_143110_438_24362 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143111_587_12348
+ echo pp20221021_143111_587_12348
+ docker run --name pp20221021_143111_587_12348 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve /usr/local/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=mauve-align --output-guide-tree=mauve-align.guide_tree --backbone-output=mauve-align.backbone output_for_mauve/q.fa.gb output_for_mauve/ref.fa.gb
Storing raw sequence at /tmp/rawseq1.000
Sequence loaded successfully.
output_for_mauve/q.fa.gb 12142016 base pairs.
Storing raw sequence at /tmp/rawseq1.001
Sequence loaded successfully.
output_for_mauve/ref.fa.gb 12071326 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
Sorted mer list loaded successfully
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
using default bp penalty: 164705
using default bp estimate min score: 494115
Starting with 69309 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.0932985
0.0932985 0
Writing guide tree to mauve-align.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 2149 initial LCBs
Using scaled bp penalty: 333953
Pair (0,1) has 4 well-supported breakpoints
genome content distance matrix:
0 0.0932985
0.0932985 0
bp distance matrix:
0.9 0.0198895
0.0198895 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68120 tracking matches
There are 136240 / 204360 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 2163 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 14 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 9.70802e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 104 new matches outside LCBs
0,0 has an additional 1813 matches
Restoring backed up alignment tree...
1,0 has 1813 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68704 tracking matches
There are 137408 / 206112 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 1081 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 13 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 9.70802e+08, new anchor score: 9.6729e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 4 superintervals
root alignment length: 13000370
Organisms have 38.4% GC
+ -align --output-guide-tree=mauve-align.guide_tree --backbone-output=mauve-align.backbone output_for_mauve/q.fa.gb output_for_mauve/ref.fa.gb
/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve: 行 71: -align: コマンドが見つかりません
++ onerror 71
++ status=127
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
++ line=71
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve [Line 71]: Status 127
PID: 382848
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/Comparative-genomics~make-align-for-mauve
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~make-align-for-mauve
------------------------------------------------------------
PID: 382846
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/ref.fa
1 /yoshitake/test/Comparative-genomics~make-align-for-mauve/input_1/q.fa
biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7-mauve centos:centos6 quay.io/biocontainers/emboss:6.6.0--h8719169_4 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/minimap2:2.16--h84994c4_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
+ set -o pipefail
+ mkdir -p reformat_fasta
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//ref.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//ref.fa '|sed' 's/\r//g' '>' reformat_fasta/ref.fa
+ for i in '`find $input_1/|egrep "[.](fa|fasta|fsa|fna)$"||true`'
++ basename input_1//q.fa
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1 fastareformat input_1//q.fa '|sed' 's/\r//g' '>' reformat_fasta/q.fa
++ find input_1//
++ egrep '[.](fa|fasta|fsa|fna)[.]gz$'
++ true
+ awk '{if(old!=""){print old"\t"$1}else{print $1}; old=$1}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo reformat_fasta/q.fa
+ xargs -I '{}' -P 8 bash -c '{}'
++ find reformat_fasta
++ egrep '[.](fa|fasta|fsa|fna)$'
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/ref.fa
+ for i in '`find reformat_fasta|egrep "[.](fa|fasta|fsa|fna)$"||true`'
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/yoshitake/test/Comparative-genomics~make-align-for-mauve/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -u 2007:600 -i --rm biocontainers/samtools:v1.7.0_cv4 samtools faidx reformat_fasta/q.fa
+ mkdir -p output_for_mauve
++ head -n 1 list.txt
+ i=reformat_fasta/ref.fa
+ cat reformat_fasta/ref.fa.fai
+ awk '-F\t' '{print $1"\t1"}'
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143553_353_23345
+ echo pp20221021_143553_353_23345
+ docker run --name pp20221021_143553_353_23345 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">ref.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin ref.fa.txt
++ basename reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143554_325_28569
+ echo pp20221021_143554_325_28569
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_143554_325_28569 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence ref.fa.txt2 -outseq ref.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/ref.fa
++ basename reformat_fasta/ref.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; if($2==1){str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"}else{str=str" CDS complement("start".."start+len[$1]-1")\n /gene=\""$1" "$2"\"\n"}; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/ref.fa.fai ref.fa.txt ref.fa.txt2.gb
++ basename reformat_fasta/ref.fa
+ tail -n+2 list.txt
+ read k
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 2
+ i=reformat_fasta/q.fa
++ echo 'reformat_fasta/ref.fa reformat_fasta/q.fa'
++ cut -f 1
+ j=reformat_fasta/ref.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143555_340_11120
+ echo pp20221021_143555_340_11120
+ docker run --name pp20221021_143555_340_11120 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.16--h84994c4_0 minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
[M::mm_idx_gen::0.485*1.13] collected minimizers
[M::mm_idx_gen::0.638*1.63] sorted minimizers
[M::main::0.638*1.63] loaded/built the index for 16 target sequence(s)
[M::mm_mapopt_update::0.688*1.58] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 16
[M::mm_idx_stat::0.722*1.56] distinct minimizers: 2075882 (98.20% are singletons); average occurrences: 1.058; average spacing: 5.495
[M::worker_pipeline::2.860*1.91] mapped 16 sequences
[M::main] Version: 2.16-r922
[M::main] CMD: minimap2 -x asm20 -t 8 reformat_fasta/ref.fa reformat_fasta/q.fa
[M::main] Real time: 2.885 sec; CPU: 5.473 sec; Peak RSS: 0.249 GB
+ awk '-F\t' '{a[$1][$6][$5]+=$10; len[$1]=$2; len2[$6]=$7; a[$1][$6]["mid"]+=($9-$8+1)*($8+$9)/2; a[$1][$6]["n"]+=($9-$8+1)} END{for(i in a){for(j in a[i]){str="1"; if(a[i][j]["-"]>a[i][j]["+"]){str="-1"}; print i"\t"j"\t"a[i][j]["+"]+a[i][j]["-"]"\t"len[i]"\t"a[i][j]["+"]+0"\t"a[i][j]["-"]+0"\t"a[i][j]["mid"]/a[i][j]["n"]/len2[j]"\t"str}}}'
+ sort -k1,1 -k3,3gr '-t '
+ sort -k2,2 -k7,7n '-t '
+ awk 'a[$1]==0{a[$1]=1; print $0}'
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ cat q.fa_ref.fa.paf
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143558_910_30210
+ echo pp20221021_143558_910_30210
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/ref.fa
+ docker run --name pp20221021_143558_910_30210 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve awk '-F\t' 'FILENAME==ARGV[1]{n[$2]++; data[$2][n[$2]]["id"]=$1; data[$2][n[$2]]["orient"]=$8} FILENAME==ARGV[2]{if($1 in data){for(i=1; i<=length(data[$1]); i++){print data[$1][i]["id"]"\t"data[$1][i]["orient"]*$2; flag[data[$1][i]["id"]]=1}}} FILENAME==ARGV[3]&&flag[$1]!=1{print $1"\t1"}' q.fa.txt0 ref.fa.txt reformat_fasta/q.fa.fai
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143559_604_7894
+ echo pp20221021_143559_604_7894
+ docker run --name pp20221021_143559_604_7894 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'function revcomp(x, i, b){b=""; for(i=length(x);i>0;i--){switch(substr(x,i,1)){case "A":b=b"T";break; case "C":b=b"G";break; case "G":b=b"C";break; case "T":b=b"A";break; case "a":b=b"t";break; case "c":b=b"g";break; case "g":b=b"c";break; case "t":b=b"a";break; default:b=b"N";break}}; return b} BEGIN{print ">q.fa"; ORS=""} FILENAME==ARGV[1]{split($1,arr," "); seq[arr[1]]=$2} FILENAME==ARGV[2]{if($2>0){print seq[$1]}else{print revcomp(seq[$1])}} END{print "\n"}' /dev/stdin q.fa.txt
++ basename reformat_fasta/q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143600_542_5848
+ echo pp20221021_143600_542_5848
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ docker run --name pp20221021_143600_542_5848 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm quay.io/biocontainers/emboss:6.6.0--h8719169_4 seqret -sequence q.fa.txt2 -outseq q.fa.txt2.gb -osformat genbank
Read and write (return) sequences
++ basename reformat_fasta/q.fa
++ basename reformat_fasta/q.fa
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME==ARGV[2]{start+=1; str=str" CDS "start".."start+len[$1]-1"\n /gene=\""$1" "$2"\"\n"; start+=len[$1]-1} FILENAME==ARGV[3]{if(FNR==1){print $0; print "FEATURES Location/Qualifiers"; ORS=""; print str; ORS="\n"}else{print $0}}' reformat_fasta/q.fa.fai q.fa.txt q.fa.txt2.gb
++ basename reformat_fasta/q.fa
+ read k
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221021_143601_641_17409
+ echo pp20221021_143601_641_17409
+ docker run --name pp20221021_143601_641_17409 -v /yoshitake/test/Comparative-genomics~make-align-for-mauve:/yoshitake/test/Comparative-genomics~make-align-for-mauve -w /yoshitake/test/Comparative-genomics~make-align-for-mauve -u 2007:600 -i --rm c2997108/centos7:metacor7-mauve /usr/local/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=mauve-align --output-guide-tree=mauve-align.guide_tree --backbone-output=mauve-align.backbone output_for_mauve/q.fa.gb output_for_mauve/ref.fa.gb
Storing raw sequence at /tmp/rawseq1.000
Sequence loaded successfully.
output_for_mauve/q.fa.gb 12142016 base pairs.
Storing raw sequence at /tmp/rawseq1.001
Sequence loaded successfully.
output_for_mauve/ref.fa.gb 12071326 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
Sorted mer list loaded successfully
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
using default bp penalty: 164705
using default bp estimate min score: 494115
Starting with 69309 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.0932985
0.0932985 0
Writing guide tree to mauve-align.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 2149 initial LCBs
Using scaled bp penalty: 333953
Pair (0,1) has 4 well-supported breakpoints
genome content distance matrix:
0 0.0932985
0.0932985 0
bp distance matrix:
0.9 0.0198895
0.0198895 0.9
Aligning...
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68120 tracking matches
There are 136240 / 204360 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 2163 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 14 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 9.70802e+08
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 104 new matches outside LCBs
0,0 has an additional 1813 matches
Restoring backed up alignment tree...
1,0 has 1813 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 68704 tracking matches
There are 137408 / 206112 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 1081 pairwise LCBs
scaling bp penalty by conservation weight:
0.0932985
scaling bp penalty by bp weight:
0.0198895
Greedy BPE
Scoring with scaled breakpoint penalty: 106934
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..done
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 13 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 9.70802e+08, new anchor score: 9.6729e+08
propagating ancestral breakpoints
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 4 superintervals
root alignment length: 13000370
Organisms have 38.4% GC
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 385034