hicCorrectMatrix npx not supported

Question

[lea.jessop]

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.

Answer 1

[Devon Ryan]

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?