Question: hicCorrectMatrix npx not supported
0
gravatar for lea.jessop
2.5 years ago by
lea.jessop0
lea.jessop0 wrote:

I'm trying to run the Correction of the Hi-C matrix generated from hicBuildMatrix, but I get a flie format not supported error.

Any ideas why this is happening?

$ hicCorrectMatrix diagnostic_plot -m hic_matrix.npz.h5 -o hic_corrected.npz
Number of poor regions to remove: 32424
{'chr8_gl000197_random': 3, 'chr21_gl000210_random': 1, 'chrUn_gl000227': 10, 'chr6_apd_hap1': 462, 'chrUn_gl000220': 2, 'chrY': 5722, 'chrX': 879, 'chr13': 1961, 'chr12': 349, 'chr11': 421, 'chr10': 560, 'chr17': 429, 'chr16': 1237, 'chr15': 2219, 'chr14': 1948, 'chr19': 359, 'chr18': 339, 'chr9_gl000198_random': 5, 'chrUn_gl000228': 9, 'chrUn_gl000239': 2, 'chrUn_gl000238': 1, 'chr22': 1691, 'chrUn_gl000233': 2, 'chrUn_gl000232': 1, 'chr6_mann_hap4': 454, 'chrUn_gl000230': 2, 'chrUn_gl000237': 3, 'chrUn_gl000236': 3, 'chrUn_gl000213': 15, 'chr17_gl000204_random': 2, 'chr4_gl000194_random': 3, 'chrUn_gl000215': 13, 'chrUn_gl000217': 9, 'chr6_qbl_hap6': 422, 'chr1_gl000192_random': 8, 'chr7': 467, 'chrUn_gl000223': 15, 'chr6': 852, 'chr4_ctg9_hap1': 55, 'chrUn_gl000222': 2, 'chr17_ctg5_hap1': 142, 'chr6_ssto_hap7': 461, 'chr11_gl000202_random': 2, 'chr19_gl000209_random': 6, 'chr6_dbb_hap3': 453, 'chr17_gl000206_random': 5, 'chr20': 359, 'chr21': 1335, 'chr6_mcf_hap5': 466, 'chr17_gl000205_random': 1, 'chr6_cox_hap2': 465, 'chr4_gl000193_random': 2, 'chr9_gl000200_random': 19, 'chr5': 425, 'chr4': 421, 'chr3': 368, 'chr2': 604, 'chr1': 2645, 'chr9_gl000199_random': 4, 'chrUn_gl000225': 1, 'chrUn_gl000226': 1, 'chr9_gl000201_random': 3, 'chr8_gl000196_random': 4, 'chrUn_gl000221': 5, 'chr9': 2855, 'chr8': 415, 'chrUn_gl000248': 1, 'chrUn_gl000249': 4, 'chrUn_gl000246': 3, 'chrUn_gl000247': 1, 'chrUn_gl000244': 3, 'chrUn_gl000245': 4, 'chrUn_gl000242': 2, 'chrUn_gl000243': 2}

mad threshold -2.65237205882
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/bin/hicCorrectMatrix", line 7, in <module>
    main()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/hicexplorer/hicCorrectMatrix.py", line 520, in main
    plot_total_contact_dist(ma, args)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/hicexplorer/hicCorrectMatrix.py", line 455, in plot_total_contact_dist
    plt.savefig(args.plotName)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/pyplot.py", line 697, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/figure.py", line 1573, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2153, in print_figure
    canvas = self._get_output_canvas(format)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2093, in _get_output_canvas
    '%s.' % (format, ', '.join(formats)))
ValueError: Format "npz" is not supported.
Supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz.
hicexplorer • 613 views
ADD COMMENTlink modified 2.5 years ago by Devon Ryan94k • written 2.5 years ago by lea.jessop0
0
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

You've specified the diagnostic_plot subcommand, so -o specifies an output file. You will need to specify one of the file extensions mentioned in the error message.

Perhaps you meant the correct subcommand instead?

ADD COMMENTlink written 2.5 years ago by Devon Ryan94k
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