HiC-Pro-3.1.0 container: ICE normalization not working

[salvzzz]

Hi! I have been trying to run the tutorial with the Dixon test dataset but can't solve an issue with ICE.

• I have created a docker container with the 3.1.0. version (building it from the dockerfile provided here).
• I have converted the docker container to a singularity image.
• I have kept the default settings in the config file (just added bowtie2 index created from hg38.analysisSet.fa)
• Running: yes "yes" | singularity exec $CONTAINER /HiC-Pro_3.1.0/bin/HiC-Pro -i ${INPUT} -o ${OUTDIR} -c ${CONFIG}
• This correctly produced outputs including raw matrix files, but the last step with ICE normalization did not work.

Raw matrix files look small. Are they supposed to be this size? For instance, for _dixon_2M500000.matrix is just 9KB and contains only 398 rows that look like this 2147483648 2147483649 185. The _dixon2M.allValidPairs is about 7000KB. Why is the last step not working with the test dataset?

I have tried to extract both ice and iced_norm.sh files to run them directly. I provided the above-mentioned matrix file as input and retried, but still the code does not work and - unless there are issues in the code - I suspect that something could be wrong with the input matrix.

Could you help me please? Thank you in advance!

[salvzzz]

Problem Solved. The format of the Chromosome Sizes file was not correct and messed up the matrix. Thanks.