Closed biozzq closed 3 years ago
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.
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
Hello,
Ah! In the -chrFile, instead of formatting like this...
chr10
chr11
...
X
Don't include the "chr" tags:
10
11
...
X
Dear all,
Thank you. It is Ok now.
Best wishes, Zheng zhuqing
Dear all,
When running dcHiC, an error occurred to me, likes following:
my command is as following:
python /path/dchic.py -res 100000 -inputFile input.txt -chrFile chr.txt -input 2 -genome mm10 -alignData /mm10/goldenpathData -keepIntermediates 1 -blacklist /mm10/mm10-blacklist.v2.bed
Best wishes, Zheng zhuqing