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ay-lab avatar ay-lab commented on August 26, 2024

Hello,

Can you list your O/E correlation matrix directory and check that it has all of these files? For example, in "mm8WF-1_mat", there should be these files:

mm8WF-1_mat 
    chr1.matrix
    chr2.matrix
    chr3.matrix 
    ...

I believe this error is occurring because dcHiC can't find the O/E matrices it is looking for (and am updating the runtime script to catch this error in a clearer way in the future). All of them should be in the format ("chr__.matrix"). Also, check that the chromosomes in chr.txt match the chromosomes ("chr__.matrix") in the directory.

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biozzq avatar biozzq commented on August 26, 2024

Dear @ay-lab

Yes, here is the matrix files in your mentioned directory. I also checked the chromosomes in chr.txt. Although the command failed, it also created two empty directory (chr_chr10 and pcFiles). Thank you.

ls /path/CorrelationMatrices/mm8WF-1_mat/*.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr10.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr11.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr12.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr13.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr14.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr15.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr16.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr17.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr18.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr19.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr1.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr2.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr3.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr4.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr5.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr6.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr7.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr8.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chr9.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chrMT.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chrX.matrix
/path/CorrelationMatrices/mm8WF-1_mat/chrY.matrix

Best wishes,
Zheng zhuqing

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ay-lab avatar ay-lab commented on August 26, 2024

Hello,

Ah! In the -chrFile, instead of formatting like this...

chr10
chr11
...
X

Don't include the "chr" tags:

10
11
...
X

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biozzq avatar biozzq commented on August 26, 2024

Dear all,

Thank you. It is Ok now.

Best wishes,
Zheng zhuqing

from dchic.

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