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generate_report.R have noused argument #26

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gongjingtang opened this issue Jul 26, 2021 · 0 comments
Open

generate_report.R have noused argument #26

gongjingtang opened this issue Jul 26, 2021 · 0 comments

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@gongjingtang
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Hi dear:
I am having an issue with generate_report.R script.I attempt to run TC to correct my pacbio reads.
Below are commands:
python ~/TC/TranscriptClean.py --threads 30 --sam fruit.sorted.sam --genome final.genome.fasta --spliceJns all_sample.SJ.out.tab --maxLenIndel=50 --maxSJOffset=80000 --outprefix fruit
and,I get some files, fruit_clean.fa , fruit_clean.log , fruit_clean.sam , fruit_clean.TE.log

then,i want to use generate_report.R script to visualizing TranscriptClean results,the commands as follow:
Rscript ~/TC/generate_report.R ./fruit

but,i get a error like this.
Error in read_delim(logFileTE, "\t", escape_double = FALSE, col_names = TRUE, :
unused argument (trim_ws = TRUE) Calls: main -> read_delim

if i remove the 'trim_ws = TRUE' in the script,i will get the such result
[1] "Reading log files............"
[1] "Creating tables.............."
[1] "Plot 1.................."
[1] "Plot 2.................."
[1] "Plot 3.................."
[1] "Plot 5.................."
[1] "Plot 6.................."
null device
1
there no plot 4 ,and the fruit_report.pdf don't have Noncanonical jns counts in pdf.where wrong ?could you response me?
thanks.

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