compare large genomes by dot plot using last
>ecoli
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
>Consensus_tig00000001_pilon
AATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGTGAAGCGGTAAGCGAATGGCTGTACCGCCAT
CATGATGTTCCGGCAGACGACGATGAAACGCAGGCGCTGTTACGTCGCGATTCGTTATAACCGCGAAGAAGATATCGATG
TTACGGCGAGCAGTTCAGTCTTTCCTCACTGGCACAGTACATTGATGATCAGAAGAAGTGTGGTTTGTGAAATCACCAAA
ATCGTTCCTCGGTGCCAGCGGCTTAAACCGCAGGTAGCGCTGTTTGAGGATCTGGTCTGCGCAATGATGTTGCACATTCG
CCAGCAGGCGGGCTGCGAAGCGATTACTCAGGCGGTGATTGGTCGTCCGATCAACTTCCGTGGGCTGGGCGGTGATGAAG
CACCCGAGCGCAGGGATTCTGGAACGCGCGGCGAAGCGTGCCGGATTCAGGGACGTGGTATACGAGCCGGTCGCGGCTGG
GCTGGATTACGAAGCCACCTTGCAGGAAGAAAACGGGTGCTGGTGGTGGATATCGGCGGTGGTACGACTGACTGTTCATT
GCTGCTGATGGGGCCGCAGTGGCGTTCTCGATCGTGAAGCCAGCCTGCTGGGTCACAGTGGTTGCCGTATTGGCGGTAAC
GATCTGGATATCGCGCTGGCGTTTAAAACCTGATGCCACTGCTGGGTATGGGTGGCGAAACCGAAAAGGCATCGCCCTGC
post-assemble~dotplot-by-last -c 8 -m 32 input_1/ecoli.fasta input_2/ecoli.pilon.DRR015801.fasta
pp post-assemble~dotplot-by-last -c 8 -m 32 input_1/ecoli.fasta input_2/ecoli.pilon.DRR015801.fasta
Checking the realpath of input files.
0 input_1/ecoli.fasta
0 input_2/ecoli.pilon.DRR015801.fasta
c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/centos6:2-imagemagick centos:centos6 quay.io/biocontainers/last:1418--h5b5514e_0 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
++ docker pull quay.io/biocontainers/last:1418--h5b5514e_0
1418--h5b5514e_0: Pulling from biocontainers/last
aa44502a478a: Pulling fs layer
bef3901422b5: Pulling fs layer
b6572cc046f2: Pulling fs layer
6dbbfe98ccd4: Pulling fs layer
4ca545ee6d5d: Pulling fs layer
2cf552c36491: Pulling fs layer
2cf552c36491: Waiting
4ca545ee6d5d: Waiting
6dbbfe98ccd4: Waiting
b6572cc046f2: Verifying Checksum
b6572cc046f2: Download complete
6dbbfe98ccd4: Verifying Checksum
6dbbfe98ccd4: Download complete
4ca545ee6d5d: Download complete
bef3901422b5: Verifying Checksum
bef3901422b5: Download complete
aa44502a478a: Verifying Checksum
aa44502a478a: Download complete
aa44502a478a: Pull complete
bef3901422b5: Pull complete
b6572cc046f2: Pull complete
6dbbfe98ccd4: Pull complete
4ca545ee6d5d: Pull complete
2cf552c36491: Verifying Checksum
2cf552c36491: Download complete
2cf552c36491: Pull complete
Digest: sha256:a71f7d166b5eac2618e239a90a8f793eb898d19db685aa8eccd15b63e23846ab
Status: Downloaded newer image for quay.io/biocontainers/last:1418--h5b5514e_0
quay.io/biocontainers/last:1418--h5b5514e_0
++ set +ex
+ set -o pipefail
++ echo input_1/ecoli.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/ecoli.pilon.DRR015801.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ db=input_2/ecoli.pilon.DRR015801.fasta
+ q=input_1/ecoli.fasta
++ basename input_1/ecoli.fasta
++ basename input_2/ecoli.pilon.DRR015801.fasta
+ outbase=ecoli.fasta-ecoli.pilon.DRR015801.fasta
+ cpu=8
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144048_018_21378
+ echo pp20221111_144048_018_21378
+ docker run --name pp20221111_144048_018_21378 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastdb -P8 -uNEAR -R01 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb input_2/ecoli.pilon.DRR015801.fasta
+ awk '{if($0~"^>"){n++; if(n>8){n=1}}; print $0 > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.split."n".fa"}' input_1/ecoli.fasta
++ seq 1 8
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ for i in '`seq 1 $cpu`'
+ wait
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144050_880_3672
+ echo pp20221111_144050_880_3672
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144050_880_11225
+ echo pp20221111_144050_880_11225
+ docker run --name pp20221111_144050_880_3672 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.3.fa
+ docker run --name pp20221111_144050_880_11225 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144050_881_9811
+ echo pp20221111_144050_881_9811
+ docker run --name pp20221111_144050_881_9811 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_882_14377
+ echo pp20221111_144050_882_14377
+ docker run --name pp20221111_144050_882_14377 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_883_30674
+ echo pp20221111_144050_883_30674
+ docker run --name pp20221111_144050_883_30674 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_883_11213
+ echo pp20221111_144050_883_11213
+ PPDOCNAME=pp20221111_144050_883_7322
+ echo pp20221111_144050_883_7322
+ docker run --name pp20221111_144050_883_11213 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.4.fa
++ date +%Y%m%d_%H%M%S_%3N
+ docker run --name pp20221111_144050_883_7322 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.8.fa
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144050_883_17979
+ echo pp20221111_144050_883_17979
+ docker run --name pp20221111_144050_883_17979 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_883_4779
+ echo pp20221111_144050_883_4779
+ docker run --name pp20221111_144050_883_4779 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_884_27993
+ PPDOCNAME=pp20221111_144050_885_7915
+ echo pp20221111_144050_884_27993
+ echo pp20221111_144050_885_7915
+ docker run --name pp20221111_144050_885_7915 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.fa
+ docker run --name pp20221111_144050_884_27993 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.2.fa
+ PPDOCNAME=pp20221111_144050_890_10273
+ PPDOCNAME=pp20221111_144050_887_12811
+ echo pp20221111_144050_890_10273
+ echo pp20221111_144050_887_12811
+ docker run --name pp20221111_144050_887_12811 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.7.fa
+ PPDOCNAME=pp20221111_144050_889_1532
+ docker run --name pp20221111_144050_890_10273 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.5.fa
+ echo pp20221111_144050_889_1532
+ docker run --name pp20221111_144050_889_1532 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144050_894_24598
+ echo pp20221111_144050_894_24598
+ docker run --name pp20221111_144050_894_24598 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
+ PPDOCNAME=pp20221111_144050_896_9959
+ echo pp20221111_144050_896_9959
+ docker run --name pp20221111_144050_896_9959 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.6.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.4.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.8.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.3.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.6.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.2.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.5.fa
lastal: can't open file: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.7.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144107_818_2750
+ echo pp20221111_144107_818_2750
+ docker run --name pp20221111_144107_818_2750 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 maf-convert tab ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.maf
++ seq 1 8
+ for i in '`seq 1 $cpu`'
+ cat ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.maf.tab
+ for i in '`seq 1 $cpu`'
+ cat ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.2.maf.tab
cat: ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.2.maf.tab: そのようなファイルやディレクトリはありません
++ onerror 49
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~dotplot-by-last
++ line=49
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~dotplot-by-last [Line 49]: Status 1
PID: 167007
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/post-assemble~dotplot-by-last
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~dotplot-by-last
------------------------------------------------------------
PID: 167005
pp runtime error.
Checking the realpath of input files.
0 input_1/ecoli.fasta
0 input_2/ecoli.pilon.DRR015801.fasta
c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/centos6:2-imagemagick centos:centos6 quay.io/biocontainers/last:1418--h5b5514e_0 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
++ echo input_1/ecoli.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/ecoli.pilon.DRR015801.fasta
++ wc -l
++ grep '[.]gz$'
++ true
+ '[' 0 = 1 ']'
+ db=input_2/ecoli.pilon.DRR015801.fasta
+ q=input_1/ecoli.fasta
++ basename input_1/ecoli.fasta
++ basename input_2/ecoli.pilon.DRR015801.fasta
+ outbase=ecoli.fasta-ecoli.pilon.DRR015801.fasta
+ cpu=8
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144612_283_31469
+ echo pp20221111_144612_283_31469
+ docker run --name pp20221111_144612_283_31469 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastdb -P8 -uNEAR -R01 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb input_2/ecoli.pilon.DRR015801.fasta
+ awk '{if($0~"^>"){n++; if(n>8){n=1}}; print $0 > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.split."n".fa"}' input_1/ecoli.fasta
++ sed 's/ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.//; s/.fa$//'
++ ls ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.fa
+ for i in '`ls $outbase.split.*.fa|sed '\''s/'\''"$outbase"'\''.split.//; s/.fa$//'\''`'
+ wait
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144614_554_2976
+ echo pp20221111_144614_554_2976
+ docker run --name pp20221111_144614_554_2976 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 lastal -P8 ecoli.fasta-ecoli.pilon.DRR015801.fasta.lastdb ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144614_560_27306
+ echo pp20221111_144614_560_27306
+ docker run --name pp20221111_144614_560_27306 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 last-split -m1e-6
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144629_409_1724
+ echo pp20221111_144629_409_1724
+ docker run --name pp20221111_144629_409_1724 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/last:1418--h5b5514e_0 maf-convert tab ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.maf
++ ls ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.fa
++ sed 's/ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.//; s/.fa$//'
+ for i in '`ls $outbase.split.*.fa|sed '\''s/'\''"$outbase"'\''.split.//; s/.fa$//'\''`'
+ cat ecoli.fasta-ecoli.pilon.DRR015801.fasta.split.1.maf.tab
+ ln -sf input_2/ecoli.pilon.DRR015801.fasta ecoli.fasta-ecoli.pilon.DRR015801.fasta.db.fa
+ ln -sf input_1/ecoli.fasta ecoli.fasta-ecoli.pilon.DRR015801.fasta.q.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144631_095_5833
+ echo pp20221111_144631_095_5833
+ docker run --name pp20221111_144631_095_5833 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx ecoli.fasta-ecoli.pilon.DRR015801.fasta.db.fa
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144632_011_28738
+ echo pp20221111_144632_011_28738
+ docker run --name pp20221111_144632_011_28738 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx ecoli.fasta-ecoli.pilon.DRR015801.fasta.q.fa
+ in=ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab
+ fafai1=ecoli.fasta-ecoli.pilon.DRR015801.fasta.db.fa.fai
+ fafai2=ecoli.fasta-ecoli.pilon.DRR015801.fasta.q.fa.fai
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144632_916_1068
+ echo pp20221111_144632_916_1068
+ docker run --name pp20221111_144632_916_1068 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' '
FILENAME==ARGV[1]{if($0!~"^#" && $6>=1*1000 && $11>=1*1000){if($10=="+"){aln[$2":"$7]["+"]+=$4}else if($10=="-"){aln[$2":"$7]["-"]+=$4}; aln3[$2":"$7]+=$4}}
FILENAME==ARGV[2] && $0!~"^#"{if($6>=1*1000 && $11>=1*1000){if(aln[$2":"$7]["+"]>=aln[$2":"$7]["-"]){print aln3[$2":"$7]"\t+\t"$0}else{print aln3[$2":"$7]"\t-\t"$0}}}
' ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab ./ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab
+ sort -k1,1gr -k6,6g
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144633_694_27081
+ echo pp20221111_144633_694_27081
+ docker run --name pp20221111_144633_694_27081 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' 'FILENAME==ARGV[1]{a[$4][$9]+=$6; b[$9][$4]+=$11; d[$4][$9][length(d[$4][$9])]=$0}
FILENAME==ARGV[2]{
if(n==0){
n++; for(i in a){
k=0;for(j in a[i]){
if(a[i][j]>k){
k=a[i][j]; max1[i]=j;
}
};tempavg=0; tempn=0; for(j in d[i][max1[i]]){
split(d[i][max1[i]][j],arr,"\t");
if(arr[12]=="+"){tempavg=(tempavg*tempn+(arr[10]+arr[11]/2)*arr[11])/(tempn+arr[11])}else{tempavg=(tempavg*tempn+(arr[13]-arr[10]-arr[11]/2)*arr[11])/(tempn+arr[11])};
tempn+=arr[6];
}; avg1[i]=tempavg; fmax1[max1[i]][i]=1;
}; for(i in b){
k=0;for(j in b[i]){
if(b[i][j]>k){
k=b[i][j]; max2[i]=j;
}
};tempavg=0; tempn=0; for(j in d[max2[i]][i]){
split(d[max2[i]][i][j],arr,"\t");
tempavg=(tempavg*tempn+(arr[5]+arr[6]/2)*arr[6])/(tempn+arr[6])
}; avg2[i]=tempavg; fmax2[max2[i]][i]=1;
}
};
if(check1[$4]=="" && check2[$9]==""){
check1[$4]="+"; check2[$9]=$2;
delete(dafter); delete(dbefore); delete(eafter); delete(ebefore);
if($4 in fmax2){
for(m in fmax2[$4]){
if(max2[m]==$4 && check2[m]==""){
split(d[max2[m]][m][0] ,arr,"\t");
if(arr[1]>arr[13]*0.1){
check2[m]=arr[2];
if(avg2[m]<($5+$6/2)){dbefore[m]=sprintf("%12d%s%s", avg2[m], SUBSEP, m)}else{dafter[m]=sprintf("%12d%s%s", avg2[m], SUBSEP, m)}
}
}
}};
if($9 in fmax1){
for(m in fmax1[$9]){
if(max1[m]==$9 && check1[m]==""){
split(d[m][max1[m]][0],arr,"\t");
if(arr[1]>arr[8]*0.1){
if($2=="+"){check1[m]=arr[2]}else{if(arr[2]=="+"){check1[m]="-"}else{check1[m]="+"}};
if($12=="+"){tempavg=$10+$11/2}else{tempavg=$13-$10-$11/2}
if(avg1[m]=1;m--){
split(eafter[m], arr_tmp, SUBSEP); print "info:"arr_tmp[1]"\t"check1[arr_tmp[2]]"\t"check2[$9]"\t"d[arr_tmp[2]][$9][0]
}
};
print "main:\t"check1[$4]"\t"check2[$9]"\t"$0;
for(m=1;m<=na;m++){
split(dafter[m], arr_tmp, SUBSEP); print "info:"arr_tmp[1]"\t"check1[$4]"\t"check2[arr_tmp[2]]"\t"d[$4][arr_tmp[2]][0]
};
if(check2[$9]=="+"){
for(m=1;m<=ne;m++){
split(eafter[m], arr_tmp, SUBSEP); print "info:"arr_tmp[1]"\t"check1[arr_tmp[2]]"\t"check2[$9]"\t"d[arr_tmp[2]][$9][0]
}
}else{
for(m=nd;m>=1;m--){
split(ebefore[m], arr_tmp, SUBSEP); print "info:"arr_tmp[1]"\t"check1[arr_tmp[2]]"\t"check2[$9]"\t"d[arr_tmp[2]][$9][0]
}
};
}
}' ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.da ./ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.da
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144634_396_15809
+ echo pp20221111_144634_396_15809
+ docker run --name pp20221111_144634_396_15809 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty awk '-F\t' 'FILENAME==ARGV[1]{if($7 in a){}else{a[$7][1]=tota*1; a[$7][2]=$11; a[$7][3]=$10; a[$7][4]=$2; tota+=$11;
if($2=="+"){print $7"\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xp.txt"; print ".\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xm.txt"}else{print ".\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xp.txt"; print $7"\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xm.txt"}};
if($12 in b){}else{b[$12][1]=totb*1; b[$12][2]=$16; b[$12][3]=$15; b[$12][4]=$3; totb+=$16;
if($3=="+"){print $12"\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt"; print ".\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.ym.txt"}else{print ".\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt"; print $12"\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.ym.txt"}}}
FILENAME==ARGV[2]{if($4 in a){}else{a[$4][1]=tota*1; a[$4][2]=$8; a[$4][3]="+"; a[$4][4]="+"; tota+=$8; print $4"\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xp.txt"; print ".\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xm.txt"};
if($9 in b){}else{b[$9][1]=totb*1; b[$9][2]=$13; b[$9][3]=$12; b[$9][4]=$2; totb+=$13;
if($2=="+"){print $9"\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt"; print ".\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.ym.txt"}else{print ".\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt"; print $9"\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.ym.txt"}};
if($12=="+"){ystart=$10; ywidth=$11; ylen=$13}else{ystart=$13-$10-$11; ywidth=$11; ylen=$13};
if(a[$4][4]=="+"){x1=a[$4][1]+$5; x2=a[$4][1]+$5+$6}else{x1=a[$4][1]+$8-$5; x2=a[$4][1]+$8-$5-$6};
if((b[$9][4]=="+" && $12=="+") || (b[$9][4]=="-" && $12=="-")){y1=b[$9][1]+$10; y2=b[$9][1]+$10+$11}else{y1=b[$9][1]+$13-$10; y2=b[$9][1]+$13-$10-$11}; print x1"\t"x2"\t"y1"\t"y2}
FILENAME==ARGV[3]{if($1 in a){}else{tota+=$2; print $1"\t"tota > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xp.txt"}}
FILENAME==ARGV[4]{if($1 in b){}else{totb+=$2; print $1"\t"totb > "ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt"}}' ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.da3 ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.da ecoli.fasta-ecoli.pilon.DRR015801.fasta.db.fa.fai ecoli.fasta-ecoli.pilon.DRR015801.fasta.q.fa.fai
+ cat
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144635_099_22114
+ echo pp20221111_144635_099_22114
+ docker run --name pp20221111_144635_099_22114 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm c2997108/centos6:2-bwa-0.7.17-r1198-dirty R --vanilla
R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> xp=read.table("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xp.txt")
> xm=read.table("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.xm.txt")
> yp=read.table("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.yp.txt")
> ym=read.table("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.ym.txt")
> if(nrow(xp)==1){xp2=0}else{xp2=c(0,xp[1:(nrow(xp)-1),2])}
> if(nrow(xm)==1){xm2=0}else{xm2=c(0,xm[1:(nrow(xm)-1),2])}
> if(nrow(yp)==1){yp2=0}else{yp2=c(0,yp[1:(nrow(yp)-1),2])}
> if(nrow(ym)==1){ym2=0}else{ym2=c(0,ym[1:(nrow(ym)-1),2])}
> #png("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.png",width=4000,height=4000)
> #library("Cairo")
> #CairoPNG("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.png",width=4000,height=4000)
> pdf("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.pdf",width=30,height=30)
> b=read.table("ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.da4")
> par(mar=c(10,10,4,4))
> plot(c(0,max(xp[,2])),c(0,max(yp[,2])),col="white",xaxt="n",yaxt="n", xlab="", ylab="")
> axis(1,xp[,2],lab=F)
> axis(2,yp[,2],lab=F)
> for(i in 1:dim(xp)[1]){abline(v=xp[i,2], col='gray', lty=2)}
> abline(v=0, col='gray', lty=2)
> #abline(v=max(b[,1:2]), col='gray', lty=2)
> for(i in 1:dim(yp)[1]){abline(h=yp[i,2], col='gray', lty=2)}
> abline(h=0, col='gray', lty=2)
> #abline(h=max(b[,3:4]), col='gray', lty=2)
> for(i in 1:dim(b)[1]){if((b[i,2]-b[i,1])/1.0*(b[i,4]-b[i,3])/1.0>0){par(col="red")}else{par(col="blue")}; lines(c(b[i,1],b[i,2]),c(b[i,3],b[i,4]),lwd=1)}
> par(xpd=TRUE, col="red")
> text(xp[,2]-(xp[,2]-xp2)/2,par("usr")[3]-1.5,xp[,1],adj=c(1,1),srt=45)
> text(par("usr")[1]-1.5,yp[,2]-(yp[,2]-yp2)/2,yp[,1],adj=c(1,1),srt=45)
> par(xpd=TRUE, col="blue")
> text(xm[,2]-(xm[,2]-xm2)/2,par("usr")[3]-1.5,xm[,1],adj=c(1,1),srt=45)
> text(par("usr")[1]-1.5,ym[,2]-(ym[,2]-ym2)/2,ym[,1],adj=c(1,1),srt=45)
> dev.off()
null device
1
>
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20221111_144636_233_20215
+ echo pp20221111_144636_233_20215
+ docker run --name pp20221111_144636_233_20215 -v /yoshitake/test/post-assemble~dotplot-by-last:/yoshitake/test/post-assemble~dotplot-by-last -w /yoshitake/test/post-assemble~dotplot-by-last -u 2007:600 -i --rm c2997108/centos6:2-imagemagick convert -density 300 ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.pdf ecoli.fasta-ecoli.pilon.DRR015801.fasta.maf.tab.png
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 169800