DESeq2 analysis
gene_id 0010_1.fastq 0012_1.fastq 0014_1.fastq 0015_1.fastq 0016_1.fastq 0017_1.fastq 0021_1.fastq 0024_1.fastq 0025_1.fastq 0026_1.fastq 0032_1.fastq 0035_1.fastq 0041_1.fastq 0042_1.fastq 0046_1.fastq 0050_1.fastq 0063_1.fastq 0066_1.fastq 0067_1.fastq 0069_1.fastq 0073_1.fastq 0074_1.fastq 0080_1.fastq 0081_1.fastq 0083_1.fastq 0085_1.fastq 0086_1.fastq 0087_1.fastq 0088_1.fastq 0089_1.fastq 0094_1.fastq 0095_1.fastq 0096_1.fastq 0097_1.fastq 0098_1.fastq 0102_1.fastq 0103_1.fastq 0104_1.fastq 9250_1.fastq 9303_1.fastq fin8220_1.fastq fin8241_1.fastq
MSTRG.34956 0 0 1.67825 0.841872 0.51571 0 0 0 0 0 1.19179 0 0 0 0 0 2.22818 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.58743 0 0 0 0 2.16523 0 0 0 0 0
MSTRG.33635 0.8125 0 0 0 0.952206 0 1.02941 0.084559 0 0.555147 1.14016 0.371324 0 1.03676 2.20588 0.503676 0 0.055147 1.52941 0 0 0 0 5.45221 0 0.191176 0 0 0.088235 0 0 0.058824 0 0.966912 0 0.669118 1.57721 2.61029 0 0 0 0
MSTRG.34957 0 0.349481 0 0 0 0 0 0 0 0 0 0 0 0 0 0.279123 0.920415 0 0 0 0 0 0 0.179931 0 0 0 0 0 0 0 0 0 0.219723 3.35294 0 0 0 0 0 0 0
MSTRG.33636 0.517241 0 0 0 0 0.52069 0 0.517241 0 0 1.47759 0.517241 0 0.510345 0.455172 0.496552 0 0 1.53965 0 0.255172 0 0 0 0 0 0.512069 0 0 0 0 0 0.194828 0.437931 0.025862 0.517241 1.23104 1.06724 0.225862 0 1.13597 0.218966
MSTRG.34958 0.476948 0 0 0 0 0.91256 0.329094 0 0 0 0 0.45151 0.45787 0 0 0.952305 0.839428 0.403816 1.8601 0 0.235294 0.475358 0 0.470588 0 0.146264 0.440382 0 0.699523 2.12719 0.236884 0.267091 0.620032 0.915739 0 0.406995 0.91097 0.244833 1.37997 0 0.922099 0
MSTRG.33637 8.76232 14.7562 7.40916 15.2814 11.9498 7.58117 5.27547 19.5882 8.16143 4.63251 9.4 6.13842 7.48348 11.8151 6.73134 13.8355 13.1805 7.16488 12.4116 4.40255 4.95846 11.1834 7.56257 11.8422 7.06995 10.0331 9.8606 9.28109 8.04729 13.3893 7.5768 4.89631 6.78818 10.9112 8.54253 11.2956 9.72315 8.13215 12.1456 5.36823 10.9889 10.7606
MSTRG.34959 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSTRG.33638 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.37895 0 0 1.42749 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSTRG.32000 48.3219 56.5226 38.3145 67.8422 73.1224 32.1719 49.1824 88.3027 37.3264 36.0939 50.4939 52.2885 52.2132 52.5532 36.7729 85.1511 37.2282 54.4083 56.4022 23.0667 18.1345 59.9655 50.6956 72.1771 40.3438 38.1944 59.5931 33.2765 42.9829 91.9969 61.339 40.5121 51.9577 67.4603 50.278 67.3721 50.8645 36.9446 62.7158 34.0289 49.6916 33.7935
id condition
0010_1.fastq male_short
0016_1.fastq female_short
0021_1.fastq female_long
0024_1.fastq male_long
0032_1.fastq male_long
0035_1.fastq female_short
0050_1.fastq female_short
0063_1.fastq female_short
0069_1.fastq male_long
id condition
0010_1.fastq.gz male_short
0016_1.fastq.gz female_short
0021_1.fastq.gz female_long
0024_1.fastq.gz male_long
0032_1.fastq.gz male_long
0035_1.fastq.gz female_short
0050_1.fastq.gz female_short
0063_1.fastq.gz female_short
0069_1.fastq.gz male_long
statistics~DESeq2 -c 8 -m 32 input_1/fin.qiu.genes.count_table input_2/Qiu.fin2.txt
pp statistics~DESeq2 -c 8 -m 32 input_1/fin.qiu.genes.count_table input_2/Qiu.fin2.txt
Checking the realpath of input files.
0 input_1/fin.qiu.genes.count_table
0 input_2/Qiu.fin2.txt
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2
script: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/statistics~DESeq2 "$scriptdir"/statistics~scatter_with_variance
c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6
using docker
++ docker pull c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4: Pulling from c2997108/centos7
8ba884070f61: Pulling fs layer
90629ce61298: Pulling fs layer
251dfbb6a15d: Pulling fs layer
e3d92a7f13dc: Pulling fs layer
e768b701dfbb: Pulling fs layer
4cc4525b8a1e: Pulling fs layer
439be8403c2c: Pulling fs layer
7ee91115c79b: Pulling fs layer
ab97148a63e3: Pulling fs layer
e3d92a7f13dc: Waiting
e768b701dfbb: Waiting
04a623cfc77d: Pulling fs layer
4cc4525b8a1e: Waiting
ab97148a63e3: Waiting
04a623cfc77d: Waiting
7ee91115c79b: Waiting
439be8403c2c: Waiting
8ba884070f61: Verifying Checksum
8ba884070f61: Download complete
e3d92a7f13dc: Verifying Checksum
e3d92a7f13dc: Download complete
e768b701dfbb: Verifying Checksum
e768b701dfbb: Download complete
4cc4525b8a1e: Download complete
439be8403c2c: Verifying Checksum
439be8403c2c: Download complete
7ee91115c79b: Verifying Checksum
7ee91115c79b: Download complete
ab97148a63e3: Verifying Checksum
ab97148a63e3: Download complete
04a623cfc77d: Verifying Checksum
04a623cfc77d: Download complete
8ba884070f61: Pull complete
251dfbb6a15d: Verifying Checksum
251dfbb6a15d: Download complete
90629ce61298: Verifying Checksum
90629ce61298: Download complete
90629ce61298: Pull complete
251dfbb6a15d: Pull complete
e3d92a7f13dc: Pull complete
e768b701dfbb: Pull complete
4cc4525b8a1e: Pull complete
439be8403c2c: Pull complete
7ee91115c79b: Pull complete
ab97148a63e3: Pull complete
04a623cfc77d: Pull complete
Digest: sha256:0d79ccb1e305397c9ad1ad7681a1f8992250f53aaef963aba53490e9b0916eaf
Status: Downloaded newer image for c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
docker.io/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
++ set +ex
++ docker pull centos:centos6
centos6: Pulling from library/centos
ff50d722b382: Pulling fs layer
ff50d722b382: Verifying Checksum
ff50d722b382: Download complete
ff50d722b382: Pull complete
Digest: sha256:a93df2e96e07f56ea48f215425c6f1673ab922927894595bb5c0ee4c5a955133
Status: Downloaded newer image for centos:centos6
docker.io/library/centos:centos6
++ set +ex
+ set -o pipefail
+ script=run-DESeq2.R
+ inputmatrix=input_1/fin.qiu.genes.count_table
+ sed 's/\r//g'
+ cat input_2/Qiu.fin2.txt
+ sed '/^$/d'
+ sed 's/ \+/\t/g; s/\t\+/\t/g; s/\t\+$//; s/[.]gz\t/\t/'
+ awk '-F\t' '{gsub(/[^A-Za-z0-9._\t-]/,"_",$0); print $0}'
++ basename input_1/fin.qiu.genes.count_table
++ basename input_1/fin.qiu.genes.count_table
+ inputsamplematrix=input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
+ g1=
+ g2=
+ '[' '' = '' ']'
++ tail -n+2 input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
++ uniq
++ head -n 1
++ cut -f 2
++ sort -V
+ g1=female_long
+ '[' '' = '' ']'
++ head -n 2
++ uniq
++ sort -V
++ cut -f 2
++ tail -n 1
++ tail -n+2 input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
+ g2=female_short
+ p=0.05
++ basename input_1/fin.qiu.genes.count_table
+ outputfile=DESeq2.fin.qiu.genes.count_table
++ basename input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
++ basename input_1/fin.qiu.genes.count_table
+ samplex=DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x
++ basename input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
++ basename input_1/fin.qiu.genes.count_table
+ sampley=DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y
++ basename input_1/fin.qiu.genes.count_table
+ outputfilexup=result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt
++ basename input_1/fin.qiu.genes.count_table
+ outputfileyup=result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt
+ '[' '' = '' ']'
+ annotationfile=input_1/fin.qiu.genes.count_table
+ cat
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230907_180338_846_30620
+ echo pp20230907_180338_846_30620
++ id -u
++ id -g
+ docker run --name pp20230907_180338_846_30620 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 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.
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
> colData <- read.table("input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt", header=T, row.names=1, sep="\t")
> countData=round(read.table("input_1/fin.qiu.genes.count_table",sep="\t",header=T,row.names=1))
> mydata=data.frame("group"=as.character(colData[,1]),stringsAsFactors=F)
> dds <- DESeqDataSetFromMatrix(countData = countData, colData = mydata, design = ~ group)
Error in DESeqDataSetFromMatrix(countData = countData, colData = mydata, :
ncol(countData) == nrow(colData) is not TRUE
Calls: DESeqDataSetFromMatrix -> stopifnot
Execution halted
+ true
+ '[' '!' -e DESeq2.fin.qiu.genes.count_table ']'
+ touch DESeq2.fin.qiu.genes.count_table
+ cut -f 1
+ tail -n+2 DESeq2.fin.qiu.genes.count_table
+ awk '-F\t' -v g1=female_long '$2==g1{print $1}' input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
+ awk '-F\t' -v g2=female_short '$2==g2{print $1}' input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt
+ bash /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/statistics~scatter_with_variance -x female_long -y female_short input_1/fin.qiu.genes.count_table DESeq2.fin.qiu.genes.count_table.id DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y
Checking the realpath of input files.
0 input_1/fin.qiu.genes.count_table
0 DESeq2.fin.qiu.genes.count_table.id
0 DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x
0 DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y
c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6
using docker
+ set -o pipefail
+ countmat=input_1/fin.qiu.genes.count_table
+ sigmat=DESeq2.fin.qiu.genes.count_table.id
+ listx=DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x
+ listy=DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y
+ label_x=female_long
+ label_y=female_short
+ p=0.05
++ basename input_1/fin.qiu.genes.count_table
++ basename DESeq2.fin.qiu.genes.count_table.id
+ output=fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id
+ cat input_1/fin.qiu.genes.count_table
+ awk '-F\t' 'FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}} FILENAME==ARGV[2]{if(FNR==1){print $0}else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*1000*1000}; print "\n"}}' /dev/stdin input_1/fin.qiu.genes.count_table
+ cat DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2]{if(FNR==1){for(i=1;i<=NF;i++){if(a[$i]==1){b[i]=1}}}; ORS=""; print $1; for(i=2;i<=NF;i++){if(b[i]==1){print "\t"$i}}; print "\n"}' /dev/stdin fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm
+ cat DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2]{if(FNR==1){for(i=1;i<=NF;i++){if(a[$i]==1){b[i]=1}}}; ORS=""; print $1; for(i=2;i<=NF;i++){if(b[i]==1){print "\t"$i}}; print "\n"}' /dev/stdin fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm
+ cat DESeq2.fin.qiu.genes.count_table.id
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_x
+ cat DESeq2.fin.qiu.genes.count_table.id
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_y
+ cat
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230907_180403_481_4622
+ echo pp20230907_180403_481_4622
++ id -u
++ id -g
+ docker run --name pp20230907_180403_481_4622 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 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.
>
> label_x="female_long"
> label_y="female_short"
> file_data_x="fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_x"
> file_data_y="fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_y"
> file_sig_data_x="fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_x_sig"
> file_sig_data_y="fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_y_sig"
> data_x=round(read.table(file_data_x,sep="\t",header=T,row.names=1))
> data_y=round(read.table(file_data_y,sep="\t",header=T,row.names=1))
> sig_data_x=read.table(file_sig_data_x,sep="\t",header=T,row.names=1)
> if(dim(sig_data_x)[1]!=0){sig_data_x=round(sig_data_x)}
> sig_data_y=read.table(file_sig_data_y,sep="\t",header=T,row.names=1)
> if(dim(sig_data_y)[1]!=0){sig_data_y=round(sig_data_y)}
> mean_data_x=apply(data_x,1,mean)
> mean_data_y=apply(data_y,1,mean)
> if(dim(data_x)[2]>1){
+ dx=apply(data_x,1,function(i){return(abs(qt(0.05/2, length(i)-1)) * sd(i) / sqrt(length(i)))})
+ }else{
+ dx=0
+ }
> if(dim(data_y)[2]>1){
+ dy=apply(data_y,1,function(i){return(abs(qt(0.05/2, length(i)-1)) * sd(i) / sqrt(length(i)))})
+ }else{
+ dy=0
+ }
> vx=dx/mean_data_x
> vy=dy/mean_data_y
> vx[is.na(vx)]=0
> vy[is.na(vy)]=0
> #total_var_data=sqrt(dx^2+dy^2)/sqrt(mean_data_x^2+mean_data_y^2)
> #total_var_data[is.na(total_var_data)]=0
> total_var_data=sqrt(vx^2+vy^2)
> mean_sig_data_x=apply(sig_data_x,1,mean)
> mean_sig_data_y=apply(sig_data_y,1,mean)
> min_x=min(mean_data_x[mean_data_x>0])/10
> min_y=min(mean_data_y[mean_data_y>0])/10
> plot_mean_data_x=mean_data_x+min_x
> plot_mean_data_y=mean_data_y+min_y
> plot_mean_sig_data_x=mean_sig_data_x+min_x
> plot_mean_sig_data_y=mean_sig_data_y+min_y
> max_x=max(plot_mean_data_x)
> max_y=max(plot_mean_data_y)
> library(Cairo)
> mainplotfunc=function(){
+ if(max(dx,dy)>0){
+ start_class=quantile(total_var_data[total_var_data>0],c(0,1,25,50,75,90,100)/100)[2]
+ end_class=quantile(total_var_data[total_var_data>0],c(0,1,25,50,75,90,100)/100)[6]
+
+ CairoPNG("fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.scatter.png",width=800,height=600)
+ num_class=22
+ library(RColorBrewer)
+ #mycol=colorRampPalette(c(rgb(0.5,0,0.2,0.4),rgb(1,0.8,0.7,1)), alpha=TRUE)(num_class)
+ colPal3 <- colorRampPalette(brewer.pal(9,"YlOrRd")[3:9])
+ mycol=colPal3(num_class)
+
+ layout(matrix(c(1,1,1,1,2),1,5))
+ par(ps = 18)
+ k=0
+ i=end_class
+ n=(total_var_data>=i)
+ xt=plot_mean_data_x[n]
+ yt=plot_mean_data_y[n]
+ plot(xt,yt,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),cex=2*(k+1)^3/num_class^3,pch=21,col=adjustcolor(mycol[k+1],0),bg=adjustcolor(mycol[k+1],1-0.4*k/num_class),xlab=label_x,ylab=label_y)
+
+ for(k in 1:(num_class-2)){
+ i=end_class+(start_class-end_class)*k/(num_class-2)
+ n=(total_var_data>=i & total_var_data=i & total_var_data=",i),pos=4)
+ }
+ k=num_class-1
+ i=min(total_var_data)
+ par(new=T)
+ plot(c(0),c(k),xlim=c(0,0),ylim=c(-1,num_class),col=adjustcolor(mycol[k+1],0),bg=adjustcolor(mycol[k+1],1-0.4*k/num_class),pch=21,cex=2*(k+1)^3/num_class^3,bty="n",axes=F,xlab="",ylab="")
+ text(c(0.05),c(k),paste(">=",i),pos=4)
+ text(0,num_class+0.2,"95%conf/mean")
+ par(new=T)
+ plot(c(-0.3),c(-1),xlim=c(0,0),ylim=c(-1,num_class),col="green",cex=1,bty="n",axes=F,xlab="",ylab="")
+ text(c(-0.3),c(-1),paste("significant"),pos=4)
+
+ dev.off()
+ }
+ }
> subplotfunc=function(){
+ CairoPNG("fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.scatter.normal.png",width=600,height=600)
+ plot(plot_mean_data_x,plot_mean_data_y,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),cex=0.1,pch=21,col=adjustcolor("#000000",0.5),xlab=label_x,ylab=label_y)
+ par(new=T)
+ plot(plot_mean_sig_data_x,plot_mean_sig_data_y,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),col="green",cex=2,axes=F,xlab="",ylab="")
+ dev.off()
+ }
>
> wflag=0
> while(wflag<=5){
+ restry=NULL
+ restry=try(mainplotfunc(), silent = FALSE)
+ if(class(restry)!="try-error"){break}
+ try(dev.off())
+ Sys.sleep(10+runif(1, min=0,max=100)/10)
+ wflag=wflag+1
+ }
> wflag=0
> while(wflag<=5){
+ restry=NULL
+ restry=try(subplotfunc(), silent = FALSE)
+ if(class(restry)!="try-error"){break}
+ try(dev.off())
+ Sys.sleep(10+runif(1, min=0,max=100)/10)
+ wflag=wflag+1
+ }
>
>
>
+ rm -f fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_x fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_y fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_x_sig fin.qiu.genes.count_table.DESeq2.fin.qiu.genes.count_table.id.cpm_y_sig
+ post_processing
+ '[' 2 = 1 ']'
+ exit
+ awk '{if($3>=0){print $1"\tx"}else{print $1"\ty"}}'
+ tail -n+2 DESeq2.fin.qiu.genes.count_table
+ cut -f 1,7
+ awk '-F\t' 'NR==1{print -1"\t"$0} NR>1{print $2"\t"$0}'
+ cut -f 2-
+ awk '-F\t' 'NR==1{print "id\t"$0} NR>1{print $0}' DESeq2.fin.qiu.genes.count_table
+ sort -k1,1g
+ awk '-F\t' 'FILENAME==ARGV[1]{xy[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){header=$0}; res[$1]=$0} FILENAME==ARGV[3]{if(FNR==1){print header"\t"$2}else{if(xy[$1]=="x"){print res[$1]"\t"$2}}}' DESeq2.fin.qiu.genes.count_table.xy input_1/fin.qiu.genes.count_table DESeq2.fin.qiu.genes.count_table.p
+ awk '-F\t' 'FILENAME==ARGV[1]{xy[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){header=$0}; res[$1]=$0} FILENAME==ARGV[3]{if(FNR==1){print header"\t"$2}else{if(xy[$1]=="y"){print res[$1]"\t"$2}}}' DESeq2.fin.qiu.genes.count_table.xy input_1/fin.qiu.genes.count_table DESeq2.fin.qiu.genes.count_table.p
+ i=result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt
+ sed 's/\t$//'
+ awk '-F\t' -v maxlen=30000 'FILENAME==ARGV[1]{for(i=1;i<=NF;i++){n=int((length($i)-1)/maxlen)+1; if(n>a[i]){a[i]=n}}} FILENAME==ARGV[2]{if(FNR==1){ORS=""; for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print $i" (split "j")\t"}}}; print "\n"}else{for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print substr($i,(j-1)*maxlen+1,maxlen)"\t" }}}; print "\n"}}' result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt ./result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt
+ i=result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt
+ sed 's/\t$//'
+ awk '-F\t' -v maxlen=30000 'FILENAME==ARGV[1]{for(i=1;i<=NF;i++){n=int((length($i)-1)/maxlen)+1; if(n>a[i]){a[i]=n}}} FILENAME==ARGV[2]{if(FNR==1){ORS=""; for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print $i" (split "j")\t"}}}; print "\n"}else{for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print substr($i,(j-1)*maxlen+1,maxlen)"\t" }}}; print "\n"}}' result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt ./result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.xlsx
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230907_180413_500_18880
+ echo pp20230907_180413_500_18880
++ id -u
++ id -g
+ docker run --name pp20230907_180413_500_18880 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.xlsx
Start converting
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.xlsx
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230907_180418_188_26741
+ echo pp20230907_180418_188_26741
++ id -u
++ id -g
+ docker run --name pp20230907_180418_188_26741 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2 -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.xlsx
Start converting
+ rm -f DESeq2.fin.qiu.genes.count_table.id DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.x DESeq2.Qiu.fin2.txt.fin.qiu.genes.count_table.DESeq2.txt.fin.qiu.genes.count_table.y DESeq2.fin.qiu.genes.count_table.xy DESeq2.fin.qiu.genes.count_table.p result.DESeq2.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.DESeq2.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~DESeq2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 1623255