Dear Prof. Guoliang,
Recently I was trying to do some analysis of methylation data, and when I used the test data (test data with "BatMeth2testdata", download in "https://drive.google.com/open?id=1SEpvJbkjwndYcpkd39T11lrBytEq_Mac" ) in BatMeth2, There is no problem with this step: "BatMeth2 pipel --fastp ~/anaconda3/envs/fastp/bin/fastp -1 R1.fq.gz -2 R2.fq.gz -g ./batmeth2index/genome.fa -o meth -p 2 --gff ./gene.gff" . but I ran into some problems while running this step "BatMeth2 methyPlot meth.methBins.txt meth.Methygenome.pdf 0.025 meth.Methylevel.1.txt meth.function.pdf TSS TTS meth.AverMethylevel.1.txt meth.Methenrich.pdf meth.annoDensity.1.txt meth.density.pdf meth meth.mCdensity.txt meth.mCdensity.pdf meth.mCcatero.txt jcmeth.mCcatero.pdf 0.6 0.1 0.1" , as following:
Error is as follows:
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BatMeth2: MethyPlot
Dear Prof. Guoliang, Recently I was trying to do some analysis of methylation data, and when I used the test data (test data with "BatMeth2testdata", download in "https://drive.google.com/open?id=1SEpvJbkjwndYcpkd39T11lrBytEq_Mac" ) in BatMeth2, There is no problem with this step: "BatMeth2 pipel --fastp ~/anaconda3/envs/fastp/bin/fastp -1 R1.fq.gz -2 R2.fq.gz -g ./batmeth2index/genome.fa -o meth -p 2 --gff ./gene.gff" . but I ran into some problems while running this step "BatMeth2 methyPlot meth.methBins.txt meth.Methygenome.pdf 0.025 meth.Methylevel.1.txt meth.function.pdf TSS TTS meth.AverMethylevel.1.txt meth.Methenrich.pdf meth.annoDensity.1.txt meth.density.pdf meth meth.mCdensity.txt meth.mCdensity.pdf meth.mCcatero.txt jcmeth.mCcatero.pdf 0.6 0.1 0.1" , as following:
Error is as follows: #################################################################################
BatMeth2: MethyPlot
Usage: methyPlot chromsome.bins.txt chrosome.methy.distri.pdf step Infile1.from.batmeth2:methyGff out1.pdf starLabel endLabel Infile2 out2.pdf
eg: methyPlot chromsome.bins.txt chrosome.methy.distri.pdf 0.025 gene.meth.Methylevel.1.txt methlevel.pdf TSS TTS gene.meth.AverMethylevel.1.txt elements.pdf
Usage2: methyPlot chromsome.bins.txt chrosome.methy.distri.pdf 0.025 gene.meth.Methylevel.1.txt methlevel.pdf TSS TTS gene.meth.AverMethylevel.1.txt elements.pdf test.annoDensity.1.txt test.density.pdf sampleElmentName test.mCdensity.txt test.mCdensity.pdf test.mCcatero.txt test.mCcatero.pdf 0.8 0.1 0.1
Chromsome.bins.DNA.methylevel.Outfile: meth.Methygenome.pdf BatMeth2: chrom_distribution Usage: Rscript InputFile.from.Batmeth2:Split OutFile.pdf eg:Rscript chrom_distribution.batmeth2.r test.bins.txt chrosome.methy.distri.pdf null device 1 Error in par(mfrow = c(numchr * length(c), 1), mar = c(4, 4, 3, 2)) : 图形参数"mfrow"的值设得不对 停止执行 methylevel.elements.OutFile: meth.function.pdf BatMeth2: methylevel.elements Usage: Rscript methylevel.elements.r step(default:0.025) Input.from.Batmeth2:methyGff outfile.pdf xLab1 xLab2 eg: Rscript methylevel.elements.r 0.025 gene.meth.Methylevel.1.txt methlevel.pdf TSS TTS
null device 1 null device 1 null device 1 null device 1 null device 1 null device 1 null device 1 null device 1 elements.methylevel.Aver.OutFile: meth.Methenrich.pdf Batmeth2: elements.methylevel.Aver Usage:Rscript elements.methylevel.Aver.r Input.from.Batmeth2:methyGff outfile.pdf eg: Rscript elements.methylevel.Aver.r gene.meth.AverMethylevel.1.txt elements.pdf
null device 1 null device 1 BatMeth2: density_plot_with_methyl.r Usage: Rscript density_plot_with_methyl.r inputFile1 geneDensityFile output.pdf label1 eg: Rscript density_plot_with_methyl.r Cr_DJ.bins.strand.aver.txt Cr_DJ.geneBody.count.C.gffDensity.1.txt density.pdf Cr_DJ
30null device 1 null device 1 null device 1 null device 1 BatMeth2: mC Usage: Rscript thisRfile Inputfile1(mCdensity) OutFile1.pdf Inputfile2(mCcatero) OutFile2.pdf Warning message: In read.table(Infile, row.names = 1) : incomplete final line found by readTableHeader on 'meth.mCdensity.txt' null device 1 null device 1 null device 1 null device 1 awk: 命令行:1: (FILENAME=meth.1.txt.sorted.raw.cg FNR=398) 致命错误： 试图除0 awk: 命令行:1: (FILENAME=meth.1.txt.sorted.raw.chg FNR=398) 致命错误： 试图除0 awk: 命令行:1: (FILENAME=meth.1.txt.sorted.raw.chh FNR=398) 致命错误： 试图除0 #################################################################################### R installed version is 3.6.3 and the required packages are installed (including "pheatmap","xtable","ggplot2","gridExtra","grid") with the Rscricpt "install.rpackages.r" in the directory "BatMeth2-BatMeth2-v2.1/bin" .
Some of the result files are shown below: meth.methBins.txt meth.1.txt.sorted.raw.cg.txt meth.1.txt.sorted.raw.chg.txt meth.1.txt.sorted.raw.chh.txt
Thank you. Best regards, wuhainan