No matrices in ice folder

[ahmadammarmalik]

I split my fastq files and ran HiCpro; was completed sucessfully.

I placed all .validPairs in a folder and ran -s merge_persample -s build_contact_maps -s ice_norm. Once the run finished, without errors, I have matrices in the raw folder but not the ice folder. output: "Run ICE Normalization ... Logs: logs/HiC_allValidPairs/ice_100.log Logs: logs/HiC_allValidPairs/ice_500.log Logs: logs/HiC_allValidPairs/ice_1000.log Logs: logs/HiC_allValidPairs/ice_2000.log Logs: logs/HiC_allValidPairs/ice_10000.log Logs: logs/HiC_allValidPairs/ice_20000.log Logs: logs/HiC_allValidPairs/ice_50000.log Logs: logs/HiC_allValidPairs/ice_100000.log"

Also there aren't any log files in the log folder.

I had ice normalized matrices for my split fastq files.

Not sure what am I doing wrong.

[nservant]

Hi, The logs file you mentioned are not there ?? Logs: logs/HiC_allValidPairs/ice_100.log ... Could you check if the raw matrix are not empty ? Thanks

[ahmadammarmalik]

Hi, Thank you for your response.

Only have the following log files "./logs/HiC_allValidPairs/build_raw_maps.log ./logs/HiC_allValidPairs/merge_valid_interactions.log"

Have raw matrix files and the bed file. example cdhead: "130 10627525 1 130 10883442 1 130 18155322 1 130 19510095 1 130 27815372 1 131 2269993 1 "

[nservant]

Hi Difficult to help you without any error message. In theory, you should the ice binary in your path ? or in the script folder. You can try to run it by hand to normalize the data ... Best