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pughlab / VisCap

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.
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Error running VisCap #13

Open nam183 opened 5 years ago

nam183 commented 5 years ago

I am trying to run VisCap for one of my sample and getting following error, which i can not understand

"/data/Duplication/VisCap-master/MD36//MD36.sample_interval_summary" Error in mat.cov[grep("X", rownames(mat.cov), invert = TRUE), ] : incorrect number of dimensions Calls: make_matrix_from_cov_files -> colSums -> is.data.frame Execution halted

From the error i could understand there might be a problem with my sample_interval_summary file but i followed the steps shown, and my bed file also seems correct so please help me solve this error

bed file 

chr1    46654345    46654440    GENE_ID=POMGNT1_AMPL7155142781  0   +
chr1    46654426    46654514    GENE_ID=POMGNT1_AMPL7154573365  0   +
chr1    46654472    46654555    GENE_ID=POMGNT1_AMPL7154539719  0   +
chr1    46654536    46654657    GENE_ID=POMGNT1_AMPL7153085900  0   +
chr1    46654876    46655005    GENE_ID=POMGNT1_AMPL7153021413  0   +
chr1    46654952    46655042    GENE_ID=POMGNT1_AMPL7155142780  0   +
chr1    46655037    46655159    GENE_ID=POMGNT1_AMPL7153018090  0   +
chr1    46655135    46655257    GENE_ID=POMGNT1_AMPL7153085862  0   +
chr1    46655443    46655571    GENE_ID=POMGNT1_AMPL7154537337  0   +
...

sample_interval_summary file 

Target  total_coverage  average_coverage    MDDNA-201_total_cvg MDDNA-201_mean_cvg  MDDNA-201_granular_Q1   MDDNA-201_granular_median   MDDNA-201_granular_Q3   MDDNA-201_%_above_15
chr1:46654346-46654657  802 2.57    802 2.57    3   4   5   0.0
chr1:46654877-46655257  2309    6.06    2309    6.06    4   7   10  0.0
chr1:46655444-46655667  1410    6.29    1410    6.29    5   8   9   0.0
chr1:46656036-46656267  2314    9.97    2314    9.97    9   12  12  6.9
chr1:46656358-46656479  365 2.99    365 2.99    4   4   4   0.0
chr1:46657702-46657902  444 2.21    444 2.21    1   5   5   0.0
chr1:46657927-46658123  1251    6.35    1251    6.35    2   12  12  0.0
chr1:46658157-46658283  1688    13.29   1688    13.29   13  14  15  22.8
chr1:46658538-46658666  514 3.98    514 3.98    5   5   5   0.0
chr1:46658797-46659080  2914    10.26   2914    10.26   6   9   16  28.5
jeffpbruce commented 5 years ago

This may be due to overlapping regions in the bed file. We'll alter the script so it can deal with this in the near future but in the meantime please try with a bed file with no overlapping regions and see if the problem persists.

nam183 commented 5 years ago

Removed overlapping regions from bed file, still getting the same error.

migmarbor commented 2 years ago

Same problem here, any update?