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vlothec / TRASH

RepeatIdentifier
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Error: Summation of cell padding on x-direction are larger than the width for some sectors. You can e.g. set 'circos.par(cell.padding = c(0.02, 0, 0.02, 0))' or remove tiny sectors. Execution halted #8

Open Xingyu-Liao opened 1 year ago

Xingyu-Liao commented 1 year ago

Hi,

While attempting to analyze the assembly of a human sample with TRASH, an error occurred. Can you give me some hints to solve this problem? Additionally, I noticed that a '***.gff' file was generated. Dose this mean that TRs detection and recording has been successfully completed? Will this error affect the final TRs detection results? Thank you very much!

Best,

The command I used is: nohup ./TRASH_run.sh /assembly/genomic.fna --par 8 --o /data2/TRASH > /data2/TRASH/out.log 2>&1

       used   (Mb) gc trigger    (Mb)   max used    (Mb)

Ncells 2874077 153.5 8317642 444.3 39661597 2118.2 Vcells 727409116 5549.7 1632811649 12457.4 1632743435 12456.9 [1] "plotting" [1] "circos" [1] "identify chromosomes" [1] "Identify main peaks" [1] "Merge peaks" [1] "export data" [1] "Circos Plotting" [1] "set sectors" [1] "generate circos plot" [1] "1" Error: Summation of cell padding on x-direction are larger than the width for some sectors. You can e.g. set 'circos.par(cell.padding = c(0.02, 0, 0.02, 0))' or remove tiny sectors. Execution halted

vlothec commented 1 year ago

Hi, yes, I am aware of this issue. In some cases (especially large assemblies with short contigs) some generated repeats files end up empty which affects the circos plotting. It is the last step of the run, so as you noticed, other results are final and unaffected. I'll fix this in the coming weeks.

Rhia15 commented 4 months ago

Hi there, It seems that I am having the same issue, I was wondering if this has been fixed or there is anything I have to do in addition?