Error running VisCap

[nam183]

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]

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]

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

[migmarbor]

Same problem here, any update?