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daewoooo / SVbyEye

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'tilewidth' must be >= 1 and <= genome size #10

Open PengfeiInTuebingen opened 1 month ago

PengfeiInTuebingen commented 1 month ago

Dear developer, I encountered an error while plotting data with the tool. The error message is: "[pafToBins] Binning PAF alignments, binsize=10000bpError in GenomicRanges::tileGenome(seqlengths = aln.len, tilewidth = binsize, : 'tilewidth' must be >= 1 and <= genome size", I tried setting the binsize to 1000 and 10000, but the issue persists. Do you have any suggestions for resolving this? Thanks in advance! Best, PF

daewoooo commented 1 month ago

Can you please share with me an example paf file that was giving the error so I can see how to fix this?

PengfeiInTuebingen commented 1 month ago

hi, thanks for your quick reply! Somehow, it works now. i added more broad 'perc.identity.breaks', then it worked. but i can still show you my paf file here, just for some one has same issue like me:

` q.name q.len q.start q.end strand t.name t.len t.start t.end n.match aln.len mapq cg

1 chr_03 14382887 467417 523422 + chr_03 18850220 10163 74517 48039 70432 60 201M2D266M1I16M1D187M1… 2 chr_03 14382887 696336 748339 + chr_03 18850220 246022 301047 46797 56648 60 22M1I601M3D29M1D22M1I3… 3 chr_03 14382887 1596382 1636183 + chr_03 18850220 1137233 1190035 34551 55352 60 387M4D46M3I227M271I433… 4 chr_03 14382887 2022169 2062106 + chr_03 18850220 2636466 2670606 29721 42816 60 91M2I416M717D200M1D64M… 5 chr_03 14382887 10255710 10287409 + chr_03 18850220 13525588 13563582 28839 38949 60 59M3D62M1I20M3D18M2D10… 6 chr_03 14382887 13982802 14008903 + chr_03 18850220 18243390 18277170 24537 34153 60 108M1D289M1I356M7D282M… ` my command for plot is `plotMiro(paf.table = paf.46.43, binsize = 10000, perc.identity.breaks = c(70, 85, 90, 95))` Best, PF