hicCorrectMatrix npx not supported
1
0
Entering edit mode
4.1 years ago
lea.jessop • 0

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 • 845 views
ADD COMMENT
0
Entering edit mode
4.1 years ago

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 COMMENT

Login before adding your answer.

Traffic: 1921 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6