Open MichelMoser opened 2 years ago
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
Hi,
I would like to generate plots using HiCBricks to generate HiC plots for publications.
I run into troubles when loading data:
I get the following error which was mentioned in another issue as well but i couldnt figure out if it was resolved.
Any hints would be appreciated.
Thank you, Michel
file info: