error: invalid 'times' argument
MichelMoser opened this issue · 0 comments
MichelMoser commented
Hi,
I would like to generate plots using HiCBricks to generate HiC plots for publications.
I run into troubles when loading data:
cool_file1 <- "/home/momi/hg-tmp/DpnII_alto_salmon_unphased.matrix.mcool"
out_dir <- file.path("/home/momi/hg-tmp/","mcool_to_Brick_test")
dir.create(out_dir)
Create_many_Bricks_from_mcool(output_directory = out_dir,
file_prefix = "mcool_to_Brick_test",
mcool = cool_file1,
resolution = 10000,
experiment_name = "Testing mcool creation",
remove_existing = TRUE)
I get the following error which was mentioned in another issue as well but i couldnt figure out if it was resolved.
Create_many_Bricks_from_mcool(output_directory = out_dir,
+ file_prefix = "mcool_to_Brick_test",
+ mcool = cool_file1,
+ resolution = 10000,
+ experiment_name = "Testing mcool creation",
+ remove_existing = TRUE)
Provided mcool is a version 3 file.
Error in rep(chr, Offset) : invalid 'times' argument
Any hints would be appreciated.
Thank you,
Michel
file info:
> h5ls(cool_file1)
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 1000 H5I_GROUP
2 /resolutions/1000 bins H5I_GROUP
3 /resolutions/1000/bins chrom H5I_DATASET INTEGER 2758598
4 /resolutions/1000/bins end H5I_DATASET INTEGER 2758598
5 /resolutions/1000/bins start H5I_DATASET INTEGER 2758598
6 /resolutions/1000 chroms H5I_GROUP
7 /resolutions/1000/chroms length H5I_DATASET INTEGER 4011
8 /resolutions/1000/chroms name H5I_DATASET STRING 4011
9 /resolutions/1000 indexes H5I_GROUP
10 /resolutions/1000/indexes bin1_offset H5I_DATASET INTEGER 2758599
11 /resolutions/1000/indexes chrom_offset H5I_DATASET INTEGER 4012
12 /resolutions/1000 pixels H5I_GROUP
13 /resolutions/1000/pixels bin1_id H5I_DATASET INTEGER 25660039
14 /resolutions/1000/pixels bin2_id H5I_DATASET INTEGER 25660039
15 /resolutions/1000/pixels count H5I_DATASET INTEGER 25660039
16 /resolutions 10000 H5I_GROUP
17 /resolutions/10000 bins H5I_GROUP
18 /resolutions/10000/bins chrom H5I_DATASET INTEGER 277638
19 /resolutions/10000/bins end H5I_DATASET INTEGER 277638
20 /resolutions/10000/bins start H5I_DATASET INTEGER 277638
21 /resolutions/10000 chroms H5I_GROUP
22 /resolutions/10000/chroms length H5I_DATASET INTEGER 4011
23 /resolutions/10000/chroms name H5I_DATASET STRING 4011
24 /resolutions/10000 indexes H5I_GROUP
25 /resolutions/10000/indexes bin1_offset H5I_DATASET INTEGER 277639
26 /resolutions/10000/indexes chrom_offset H5I_DATASET INTEGER 4012
27 /resolutions/10000 pixels H5I_GROUP
28 /resolutions/10000/pixels bin1_id H5I_DATASET INTEGER 22843881
29 /resolutions/10000/pixels bin2_id H5I_DATASET INTEGER 22843881
30 /resolutions/10000/pixels count H5I_DATASET INTEGER 22843881
31 /resolutions 100000 H5I_GROUP
32 /resolutions/100000 bins H5I_GROUP
33 /resolutions/100000/bins chrom H5I_DATASET INTEGER 30317
34 /resolutions/100000/bins end H5I_DATASET INTEGER 30317
35 /resolutions/100000/bins start H5I_DATASET INTEGER 30317
36 /resolutions/100000 chroms H5I_GROUP
37 /resolutions/100000/chroms length H5I_DATASET INTEGER 4011
38 /resolutions/100000/chroms name H5I_DATASET STRING 4011
39 /resolutions/100000 indexes H5I_GROUP
40 /resolutions/100000/indexes bin1_offset H5I_DATASET INTEGER 30318
41 /resolutions/100000/indexes chrom_offset H5I_DATASET INTEGER 4012
42 /resolutions/100000 pixels H5I_GROUP
43 /resolutions/100000/pixels bin1_id H5I_DATASET INTEGER 15220297
44 /resolutions/100000/pixels bin2_id H5I_DATASET INTEGER 15220297
45 /resolutions/100000/pixels count H5I_DATASET INTEGER 15220297
46 /resolutions 1000000 H5I_GROUP
47 /resolutions/1000000 bins H5I_GROUP
48 /resolutions/1000000/bins chrom H5I_DATASET INTEGER 6501
49 /resolutions/1000000/bins end H5I_DATASET INTEGER 6501
50 /resolutions/1000000/bins start H5I_DATASET INTEGER 6501
51 /resolutions/1000000 chroms H5I_GROUP
52 /resolutions/1000000/chroms length H5I_DATASET INTEGER 4011
53 /resolutions/1000000/chroms name H5I_DATASET STRING 4011
54 /resolutions/1000000 indexes H5I_GROUP
55 /resolutions/1000000/indexes bin1_offset H5I_DATASET INTEGER 6502
56 /resolutions/1000000/indexes chrom_offset H5I_DATASET INTEGER 4012
57 /resolutions/1000000 pixels H5I_GROUP
58 /resolutions/1000000/pixels bin1_id H5I_DATASET INTEGER 3496226
59 /resolutions/1000000/pixels bin2_id H5I_DATASET INTEGER 3496226
60 /resolutions/1000000/pixels count H5I_DATASET INTEGER 3496226
61 /resolutions 10000000 H5I_GROUP
62 /resolutions/10000000 bins H5I_GROUP
63 /resolutions/10000000/bins chrom H5I_DATASET INTEGER 4247
64 /resolutions/10000000/bins end H5I_DATASET INTEGER 4247
65 /resolutions/10000000/bins start H5I_DATASET INTEGER 4247
66 /resolutions/10000000 chroms H5I_GROUP
67 /resolutions/10000000/chroms length H5I_DATASET INTEGER 4011
68 /resolutions/10000000/chroms name H5I_DATASET STRING 4011
69 /resolutions/10000000 indexes H5I_GROUP
70 /resolutions/10000000/indexes bin1_offset H5I_DATASET INTEGER 4248
71 /resolutions/10000000/indexes chrom_offset H5I_DATASET INTEGER 4012
72 /resolutions/10000000 pixels H5I_GROUP
73 /resolutions/10000000/pixels bin1_id H5I_DATASET INTEGER 352286
74 /resolutions/10000000/pixels bin2_id H5I_DATASET INTEGER 352286
75 /resolutions/10000000/pixels count H5I_DATASET INTEGER 352286
76 /resolutions 2000 H5I_GROUP
77 /resolutions/2000 bins H5I_GROUP
78 /resolutions/2000/bins chrom H5I_DATASET INTEGER 1380287
79 /resolutions/2000/bins end H5I_DATASET INTEGER 1380287
80 /resolutions/2000/bins start H5I_DATASET INTEGER 1380287
81 /resolutions/2000 chroms H5I_GROUP
82 /resolutions/2000/chroms length H5I_DATASET INTEGER 4011
83 /resolutions/2000/chroms name H5I_DATASET STRING 4011
84 /resolutions/2000 indexes H5I_GROUP
85 /resolutions/2000/indexes bin1_offset H5I_DATASET INTEGER 1380288
86 /resolutions/2000/indexes chrom_offset H5I_DATASET INTEGER 4012
87 /resolutions/2000 pixels H5I_GROUP
88 /resolutions/2000/pixels bin1_id H5I_DATASET INTEGER 25269260
89 /resolutions/2000/pixels bin2_id H5I_DATASET INTEGER 25269260
90 /resolutions/2000/pixels count H5I_DATASET INTEGER 25269260
91 /resolutions 25000 H5I_GROUP
92 /resolutions/25000 bins H5I_GROUP
93 /resolutions/25000/bins chrom H5I_DATASET INTEGER 112365
94 /resolutions/25000/bins end H5I_DATASET INTEGER 112365
95 /resolutions/25000/bins start H5I_DATASET INTEGER 112365
96 /resolutions/25000 chroms H5I_GROUP
97 /resolutions/25000/chroms length H5I_DATASET INTEGER 4011
98 /resolutions/25000/chroms name H5I_DATASET STRING 4011
99 /resolutions/25000 indexes H5I_GROUP
100 /resolutions/25000/indexes bin1_offset H5I_DATASET INTEGER 112366
101 /resolutions/25000/indexes chrom_offset H5I_DATASET INTEGER 4012
102 /resolutions/25000 pixels H5I_GROUP
103 /resolutions/25000/pixels bin1_id H5I_DATASET INTEGER 20285503
104 /resolutions/25000/pixels bin2_id H5I_DATASET INTEGER 20285503
105 /resolutions/25000/pixels count H5I_DATASET INTEGER 20285503
106 /resolutions 250000 H5I_GROUP
107 /resolutions/250000 bins H5I_GROUP
108 /resolutions/250000/bins chrom H5I_DATASET INTEGER 14274
109 /resolutions/250000/bins end H5I_DATASET INTEGER 14274
110 /resolutions/250000/bins start H5I_DATASET INTEGER 14274
111 /resolutions/250000 chroms H5I_GROUP
112 /resolutions/250000/chroms length H5I_DATASET INTEGER 4011
113 /resolutions/250000/chroms name H5I_DATASET STRING 4011
114 /resolutions/250000 indexes H5I_GROUP
115 /resolutions/250000/indexes bin1_offset H5I_DATASET INTEGER 14275
116 /resolutions/250000/indexes chrom_offset H5I_DATASET INTEGER 4012
117 /resolutions/250000 pixels H5I_GROUP
118 /resolutions/250000/pixels bin1_id H5I_DATASET INTEGER 10900994
119 /resolutions/250000/pixels bin2_id H5I_DATASET INTEGER 10900994
120 /resolutions/250000/pixels count H5I_DATASET INTEGER 10900994
121 /resolutions 2500000 H5I_GROUP
122 /resolutions/2500000 bins H5I_GROUP
123 /resolutions/2500000/bins chrom H5I_DATASET INTEGER 4995
124 /resolutions/2500000/bins end H5I_DATASET INTEGER 4995
125 /resolutions/2500000/bins start H5I_DATASET INTEGER 4995
126 /resolutions/2500000 chroms H5I_GROUP
127 /resolutions/2500000/chroms length H5I_DATASET INTEGER 4011
128 /resolutions/2500000/chroms name H5I_DATASET STRING 4011
129 /resolutions/2500000 indexes H5I_GROUP
130 /resolutions/2500000/indexes bin1_offset H5I_DATASET INTEGER 4996
131 /resolutions/2500000/indexes chrom_offset H5I_DATASET INTEGER 4012
132 /resolutions/2500000 pixels H5I_GROUP
133 /resolutions/2500000/pixels bin1_id H5I_DATASET INTEGER 1048644
134 /resolutions/2500000/pixels bin2_id H5I_DATASET INTEGER 1048644
135 /resolutions/2500000/pixels count H5I_DATASET INTEGER 1048644
136 /resolutions 5000 H5I_GROUP
137 /resolutions/5000 bins H5I_GROUP
138 /resolutions/5000/bins chrom H5I_DATASET INTEGER 553290
139 /resolutions/5000/bins end H5I_DATASET INTEGER 553290
140 /resolutions/5000/bins start H5I_DATASET INTEGER 553290
141 /resolutions/5000 chroms H5I_GROUP
142 /resolutions/5000/chroms length H5I_DATASET INTEGER 4011
143 /resolutions/5000/chroms name H5I_DATASET STRING 4011
144 /resolutions/5000 indexes H5I_GROUP
145 /resolutions/5000/indexes bin1_offset H5I_DATASET INTEGER 553291
146 /resolutions/5000/indexes chrom_offset H5I_DATASET INTEGER 4012
147 /resolutions/5000 pixels H5I_GROUP
148 /resolutions/5000/pixels bin1_id H5I_DATASET INTEGER 24215756
149 /resolutions/5000/pixels bin2_id H5I_DATASET INTEGER 24215756
150 /resolutions/5000/pixels count H5I_DATASET INTEGER 24215756
151 /resolutions 50000 H5I_GROUP
152 /resolutions/50000 bins H5I_GROUP
153 /resolutions/50000/bins chrom H5I_DATASET INTEGER 57489
154 /resolutions/50000/bins end H5I_DATASET INTEGER 57489
155 /resolutions/50000/bins start H5I_DATASET INTEGER 57489
156 /resolutions/50000 chroms H5I_GROUP
157 /resolutions/50000/chroms length H5I_DATASET INTEGER 4011
158 /resolutions/50000/chroms name H5I_DATASET STRING 4011
159 /resolutions/50000 indexes H5I_GROUP
160 /resolutions/50000/indexes bin1_offset H5I_DATASET INTEGER 57490
161 /resolutions/50000/indexes chrom_offset H5I_DATASET INTEGER 4012
162 /resolutions/50000 pixels H5I_GROUP
163 /resolutions/50000/pixels bin1_id H5I_DATASET INTEGER 17955214
164 /resolutions/50000/pixels bin2_id H5I_DATASET INTEGER 17955214
165 /resolutions/50000/pixels count H5I_DATASET INTEGER 17955214
166 /resolutions 500000 H5I_GROUP
167 /resolutions/500000 bins H5I_GROUP
168 /resolutions/500000/bins chrom H5I_DATASET INTEGER 9049
169 /resolutions/500000/bins end H5I_DATASET INTEGER 9049
170 /resolutions/500000/bins start H5I_DATASET INTEGER 9049
171 /resolutions/500000 chroms H5I_GROUP
172 /resolutions/500000/chroms length H5I_DATASET INTEGER 4011
173 /resolutions/500000/chroms name H5I_DATASET STRING 4011
174 /resolutions/500000 indexes H5I_GROUP
175 /resolutions/500000/indexes bin1_offset H5I_DATASET INTEGER 9050
176 /resolutions/500000/indexes chrom_offset H5I_DATASET INTEGER 4012
177 /resolutions/500000 pixels H5I_GROUP
178 /resolutions/500000/pixels bin1_id H5I_DATASET INTEGER 7263989
179 /resolutions/500000/pixels bin2_id H5I_DATASET INTEGER 7263989
180 /resolutions/500000/pixels count H5I_DATASET INTEGER 7263989
181 /resolutions 5000000 H5I_GROUP
182 /resolutions/5000000 bins H5I_GROUP
183 /resolutions/5000000/bins chrom H5I_DATASET INTEGER 4497
184 /resolutions/5000000/bins end H5I_DATASET INTEGER 4497
185 /resolutions/5000000/bins start H5I_DATASET INTEGER 4497
186 /resolutions/5000000 chroms H5I_GROUP
187 /resolutions/5000000/chroms length H5I_DATASET INTEGER 4011
188 /resolutions/5000000/chroms name H5I_DATASET STRING 4011
189 /resolutions/5000000 indexes H5I_GROUP
190 /resolutions/5000000/indexes bin1_offset H5I_DATASET INTEGER 4498
191 /resolutions/5000000/indexes chrom_offset H5I_DATASET INTEGER 4012
192 /resolutions/5000000 pixels H5I_GROUP
193 /resolutions/5000000/pixels bin1_id H5I_DATASET INTEGER 553438
194 /resolutions/5000000/pixels bin2_id H5I_DATASET INTEGER 553438
195 /resolutions/5000000/pixels count H5I_DATASET INTEGER 553438