Thanks for you developed "HiCExplorer", however I met a problem. When I tried the command to covert the format:
################
ls .matrix | while read id; do hicConvertFormat -m $id --bedFileHicpro genome_500kb.bed --inputFormat hicpro --outputFormat cool -o ${id%.}.cool; done
###############
It failed and report the error:
####################
Traceback (most recent call last):
File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[0m\x1b[01;32mFGSC_Li_merge_500000.matrix\x1b[0m'
Traceback (most recent call last):
File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[01;32mGSE82185_MII_rep12_500000.matrix\x1b[0m'
Traceback (most recent call last):
File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[01;32mGV_rep1234_merge_500000.matrix\x1b[0m'
##########################
But when I used one sample to convert the format, it worked well.
I don't know what happened?
Could you give me a hand?
Hi,
Thanks for you developed "HiCExplorer", however I met a problem. When I tried the command to covert the format: ################ ls .matrix | while read id; do hicConvertFormat -m $id --bedFileHicpro genome_500kb.bed --inputFormat hicpro --outputFormat cool -o ${id%.}.cool; done ###############
It failed and report the error: #################### Traceback (most recent call last): File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[0m\x1b[01;32mFGSC_Li_merge_500000.matrix\x1b[0m'
Traceback (most recent call last):
File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[01;32mGSE82185_MII_rep12_500000.matrix\x1b[0m'
Traceback (most recent call last):
File "/home/dell/anaconda3/envs/cooltools/bin/hicConvertFormat", line 7, in
main()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 165, in main
distance_counts, correction_factors = matrixFileHandlerInput.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load
return self.matrixFile.load()
File "/home/dell/anaconda3/envs/cooltools/lib/python3.7/site-packages/hicmatrix/lib/hicpro.py", line 19, in load
with open(self.matrixFileName, 'r') as matrix_file:
FileNotFoundError: [Errno 2] No such file or directory: '\x1b[01;32mGV_rep1234_merge_500000.matrix\x1b[0m'
##########################
But when I used one sample to convert the format, it worked well.
I don't know what happened? Could you give me a hand?
Thanks!