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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
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MethOneRegion_PDF Page content might be truncated #63

Closed StefaniaTuveri closed 1 year ago

StefaniaTuveri commented 2 years ago

Hello, I am having some problems with the function MethOneRegion. All the files are correctly generated, but the .pdf file gives me an error once opening (Page content might be truncated). The error file is empty, the output file states the following:

Subcommand: MethOneRegion /.../GC1003962.merged.rmdup.cytosine_report.txt.gz,LuminalA /.../GC1003963.merged.rmdup.cytosine_report.txt.gz,Triple- /.../GC1003965.merged.rmdup.cytosine_report.txt.gz,Her2 /.../GC1003966.merged.rmdup.cytosine_report.txt.gz,LuminalB /.../GC1002313.merged.rmdup.cytosine_report.txt.gz,WBC1 chr17:39704100-39704550 Output directory is: /.../ViewBS-0.1.9/STK Output prefix: onereg_chr17 Start calculate methylation information for target context CG Meth::OneRegion=HASH(0x2e377a8): Usage: R --vanilla --slave --input --region --output < *R /apps/leuven/skylake/2018a/software/R/4.0.2-foss-2018a-bare/lib64/R/bin/exec/R --no-echo --no-restore --file=/.../ViewBS-0.1.9/lib/Meth/OneRegion.R --args --input /.../ViewBS-0.1.9/STK/onereg_chr17_MethOneRegion_CG.txt --region 39704100-39704550 --output /.../ViewBS-0.1.9/STK/onereg_chr17_MethOneRegion_CG.pdf

Running time: 2 wallclock secs ( 0.21 usr 0.06 sys + 1.07 cusr 0.16 csys = 1.50 CPU)

xie186 commented 2 years ago

Could you please check the content in onereg_chr17_MethOneRegion_CG.txt to see whether there is any information in the file? If possible, could you please send me a test data that I can reproduce your error. Thanks.

StefaniaTuveri commented 2 years ago

This is the content of the onereg_chr17_MethOneRegion_CG.txt :

Sample chr position C_num T_num MethylationLevel LuminalA chr17 39704091 1 8 0.111111111111111 LuminalA chr17 39704092 3 4 0.428571428571429 LuminalA chr17 39704099 0 11 0 LuminalA chr17 39704100 1 5 0.166666666666667 LuminalA chr17 39704158 6 2 0.75 LuminalA chr17 39704290 2 11 0.153846153846154 LuminalA chr17 39704291 1 7 0.125 LuminalA chr17 39704304 2 10 0.166666666666667 LuminalA chr17 39704305 2 7 0.222222222222222 LuminalA chr17 39704341 7 4 0.636363636363636 LuminalA chr17 39704342 0 7 0 LuminalA chr17 39704346 7 5 0.583333333333333 LuminalA chr17 39704347 1 6 0.142857142857143