Image size related error

[shanmugavadivelps]

Hi sir, I have run qtlseq with vcf file and getting error related to image size. I am providing the errors observed during the run for your intervention. Help me to solve this.

[QTL-seq:2021-06-23 22:04:16] start to run QTL-plot. [QTL-seq:2021-06-23 22:04:16] maximum number of threads which you can use is up to 40. [QTL-seq:2021-06-23 22:04:16] start to calculate SNP-index. [QTL-seq:2021-06-23 22:04:17] no ADF or ADR field in your VCF. [QTL-seq:2021-06-23 22:04:17] strand bias filter will be skipped. [QTL-seq:2021-06-23 22:19:18] SNP-index successfully finished. [QTL-seq:2021-06-23 22:19:18] start to smooth SNP-index. [QTL-seq:2021-06-23 22:19:24] smoothing process successfully finished. [QTL-seq:2021-06-23 22:19:24] plotting now... Traceback (most recent call last): File "/home/iipruser/yes/bin/qtlplot", line 10, in sys.exit(main()) File "/home/iipruser/yes/lib/python3.8/site-packages/qtlseq/qtlplot.py", line 208, in main qp.run() File "/home/iipruser/yes/lib/python3.8/site-packages/qtlseq/qtlplot.py", line 197, in run pt.run() File "/home/iipruser/yes/lib/python3.8/site-packages/qtlseq/plot.py", line 268, in run self.plot_bulk1_SNPindex() File "/home/iipruser/yes/lib/python3.8/site-packages/qtlseq/plot.py", line 140, in plot_bulk1_SNPindex plt.savefig('{}/bulk1_SNPindex.{}'.format(self.out, self.args.format)) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/pyplot.py", line 859, in savefig res = fig.savefig(args, kwargs) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/figure.py", line 2311, in savefig self.canvas.print_figure(fname, kwargs) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 2210, in print_figure result = print_method( File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 1639, in wrapper return func(args, **kwargs) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 509, in print_png FigureCanvasAgg.draw(self) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 402, in draw self.renderer = self.get_renderer(cleared=True) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 418, in get_renderer self.renderer = RendererAgg(w, h, self.figure.dpi) File "/home/iipruser/yes/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py", line 96, in init self._renderer = _RendererAgg(int(width), int(height), dpi) ValueError: Image size of 1500x1245600 pixels is too large. It must be less than 2^16 in each direction.

[ASBioinfo]

Hi, Any fix for the above error?

[sangeeta10mar]

I am facing the same issue, please help

[ASBioinfo]

hi @sangeeta10mar For image related error coming with "pixel is too large",just go to the QTL-seq installed directory and in plot.py file make changes in self.fig_width or self.fig_height as per your requirement or optimize with other parameters in this file. plot.py mainly important for plotting the image.

[sangeeta10mar]

Thanks, I will try and then let you know.

On Wed, 2 Mar 2022, 20:06 redw0lf11, @.***> wrote:

hi @sangeeta10mar https://github.com/sangeeta10mar For image related error coming with "pixel is too large",just go to the QTL-seq installed directory and in plot.py file make changes in self.fig_width or self.fig_height as per your requirement or optimize with other parameters in this file. plot.py mainly important for plotting the image.

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[YuSugihara]

I am sorry for my late reply.

Basically, image size related error comes from contiguous reference genome because QTL-seq tries to plot each chromosome or contig to each panel.

Recently, we implemented to plot only significant chromosome or contigs when QTL-seq faced this error. So maybe you can try the latest version of QTL-seq