Warning : Matrix not found at XXX resolution

[moxqiang]

Dear all: I just want to run ice_norm，but I meet this Warning

`Run HiC-Pro 3.1.0

Fri Jul 7 15:42:19 CST 2023 Run ICE Normalization ... Logs: logs/1000000/ice_1000000.log Warning : Matrix not found at 1000000 resolution in rawdata/1000000 - skip`

my bed file : chrM 0 16569 1 chr1 0 1000000 2 chr1 1000000 2000000 3 chr1 2000000 3000000 4 chr1 3000000 4000000 5 chr1 4000000 5000000 6 chr1 5000000 6000000 7 chr1 6000000 7000000 8 chr1 7000000 8000000 9 chr1 8000000 9000000 10 chr1 9000000 10000000 11

matrix file: 0 0 1 0 1 544 0 3 1 0 22 1 0 53 1 0 54 1 0 56 1 0 62 1 0 69 1 0 87 1

config file: #######################################################################

Contact Maps

#######################################################################

BIN_SIZE = 1000000 MATRIX_FORMAT = complete

#######################################################################

Normalization

####################################################################### MAX_ITER = 100 FILTER_LOW_COUNT_PERC = 0.02 FILTER_HIGH_COUNT_PERC = 0 EPS = 0.1

my sh: /public/home/qqfu/software/HiC-Pro/hicpro/HiC-Pro_3.1.0/bin/HiC-Pro -i /public/home/qqfu/data/HPV/PCA/test_ice/output/hic_results/matrix/ \ -o /public/home/qqfu/data/HPV/PCA/test_ice/output/ \ -c /public/home/qqfu/data/HPV/PCA/test_ice/config-hicpro.txt \ -s ice_norm

Does anyone know how to go about solving this problem? Thanks!

[moxqiang]

Use other methods to complete the same operation

just use ice

[salvzzz]

Do you have multiple .matrix files in the same "./matrix/sample/raw/binsize" folder? For instance, when running HiC-Pro in allelic-mode, you'll end up having both G1.matrix and G2.matrix files in the same directory. If you get rid of one of the two matrices, then the command will work just fine, but this should be fixed.

In /HiC-Pro-3.1.0/scripts/ice_norm.sh, the command looks for one matrix, as input=$(find -L $IN_DIR/${RES_FILE_NAME}/ -name "*_$bsize.matrix*" ! -name "*iced*") This might cause the issue if you have more than one .matrix in the same directory.