In read.table(Infile, row.names = 1) : incomplete final line found by readTableHeader on './SRR8100584_sub_bathmeth2.mCdensity.txt'

[cheehowteo]

Dear Prof. Guoliang,

I tried to run BatMeth2 using the latest version and used 10000 reads from SRR8100594.sra. The latest version managed to generate most of the graph and figure except Heatmap and Differential DNA methylation analysis.

I again noticed some error in the BatMeth2 program when I checked the .run.log file. Here is the errors: Rscript /home/user/Downloads/BatMeth2/bin/mCdensity.r ./SRR8100584_sub_bathmeth2.mCdensity.txt ./SRR8100584_sub_bathmeth2.mCdensity.pdf ./SRR8100584_sub_bathmeth2.mCcatero.txt ./SRR8100584_sub_bathmeth2.mCcatero.pdf >> ./SRR8100584_sub_bathmeth2.run.log 2>&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 './SRR8100584_sub_bathmeth2.mCdensity.txt' null device 1 null device 1 null device 1 null device 1 /home/user/Downloads/BatMeth2/bin/GeneMethHeatmap ./SRR8100584_sub_bathmeth2 None 0.6 0.2 0.1 >> ./SRR8100584_sub_bathmeth2.run.log 2>&1 Usage: GeneMethHeatmap sample1 sample2[None] CG-ceil CHG-ceil CHH-ceil ./SRR8100584_sub_bathmeth2 heatmap Loading required package: pheatmap [1] "Package pheatmap is loaded correctly" Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 82595 did not have 162 elements Calls: read.table -> scan Execution halted

Thank you. Best regards, Teo SRR8100584_sub_bathmeth2.run.log

[GuoliangLi-HZAU]

Dear Teo,

Could you please provide information on these files? 'SRR8100584_sub_bathmeth2.1.txt.sorted.cg' 'SRR8100584_sub_bathmeth2.TSS.1.txt.sorted.cg' 'SRR8100584_sub_bathmeth2.TSS.1.txt.sorted.cg'

Best Regards

[cheehowteo]

Dear Prof. Guoliang,

Please find the attached files.

Thank you.

Best regards, Teo

SRR8100584_sub_bathmeth2..zip