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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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SystemError: tile cannot extend outside image #33

Closed highwire2021 closed 1 year ago

highwire2021 commented 2 years ago

Hi, Many thanks to the developers. I used use the mutmap v2.3.3 and showed "MutMap successfully finished". But the message "SystemError: tile cannot extend outside image" showed in the last line. I don't know how to deal with it.

Could you help me?

Best wishes!

YuSugihara commented 2 years ago

I am sorry for my late response.

Would you share the VCF file in 30_vcf with the command line that you ran?

highwire2021 commented 2 years ago

Thank you. The command and result as follows: ~/mutmap$ mutmap -r ref.fasta -c P7_CleanData_R1.fastq.gz,P7_CleanData_R1.fastq.gz -b R151_L2_137A37.R1.fastq.gz,R151_L2_137A37.R2.fastq.gz -n 30 -o outR151 -t 12 --species Rice [MutMap:2022-06-09 16:17:47] start to run MutMap. [MutMap:2022-06-09 16:17:47] maximum number of threads which you can use is up to 16. [MutMap:2022-06-09 16:17:47] start to index reference fasta. [MutMap:2022-06-09 16:21:27] indexing of reference successfully finished. [MutMap:2022-06-09 16:21:27] start to align reads of cultivar.0000 by BWA. [MutMap:2022-06-09 16:53:04] alignment cultivar.0000 successfully finished. [MutMap:2022-06-09 16:53:04] start to align reads of bulk.0000 by BWA. [MutMap:2022-06-09 17:41:21] alignment bulk.0000 successfully finished. [MutMap:2022-06-09 17:41:21] start to merge BAMs. [MutMap:2022-06-09 17:42:50] merging process successfully finished. [MutMap:2022-06-09 17:42:50] start to call variants. [MutMap:2022-06-09 17:46:47] variant calling successfully finished. [MutMap:2022-06-09 17:46:47] start to index VCF. [MutMap:2022-06-09 17:46:47] indexing VCF successfully finished. [MutMap:2022-06-09 17:46:48] start to run MutPlot. !!WARNING!! Number of replicates for simulation is not enough to consider multiple testing correction. Therefore, the highest SNP-index and the second highest SNP-index were selected for p99 and p95, respectively. [MutMap:2022-06-09 17:46:48] start to calculate SNP-index. [MutMap:2022-06-09 17:46:48] SNP-index successfully finished. [MutMap:2022-06-09 17:46:48] start to smooth SNP-index. [MutMap:2022-06-09 17:46:48] smoothing process successfully finished. [MutMap:2022-06-09 17:46:48] plotting now... Traceback (most recent call last): File "/home/wdk/miniconda3/envs/mutmap/bin/mutplot", line 10, in sys.exit(main()) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/mutmap/mutplot.py", line 189, in main mp.run() File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/mutmap/mutplot.py", line 178, in run pt.run() File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/mutmap/plot.py", line 164, in run plt.savefig('{}/mutmap_plot.{}'.format(self.out, self.args.format)) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/pyplot.py", line 979, in savefig res = fig.savefig(args, kwargs) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/figure.py", line 3046, in savefig self.canvas.print_figure(fname, kwargs) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2319, in print_figure result = print_method( File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 1648, in wrapper return func(args, *kwargs) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/_api/deprecation.py", line 415, in wrapper return func(inner_args, inner_kwargs) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 541, in print_png mpl.image.imsave( File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/matplotlib/image.py", line 1675, in imsave image.save(fname, pil_kwargs) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/PIL/Image.py", line 2300, in save save_handler(self, fp, filename) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/PIL/PngImagePlugin.py", line 1374, in _save ImageFile._save(im, _idat(fp, chunk), [("zip", (0, 0) + im.size, 0, rawmode)]) File "/home/wdk/miniconda3/envs/mutmap/lib/python3.10/site-packages/PIL/ImageFile.py", line 510, in _save encoder.setimage(im.im, b) SystemError: tile cannot extend outside image [MutMap:2022-06-09 17:46:49] MutMap successfully finished.

YuSugihara commented 2 years ago

Sorry for my late response.

Would you remove the option "--species Rice" and try mutplot from VCF file? We implemented that option into QTL-seq, but the results may change from what we expect.