LaZy

After ALLHiC_build stage, you will get an assembled fasta file named "groups.asm.fasta", and you need calculate the length of each sequence, then write them into chrn.list with the chromosomes which...

It means the Allele.gene.table is unreachable, please make sure this file exists first.

line 59 of partition.pl is the code for reading Allele.gene.table, and if it cannot open this file, it will raise this error "Died at line 59", so please make sure...

If you run this script with python3, the result of round function may be unexpected, I've already fix this problem, you can update it, and try again to check if...

I mean I have made some changes in the script, so you can update the ALLHiC_plot and check if it works or not.

Can you paste your list file and bin size here?

chrn.list

I added the exception check in the new version of script, and you can try it again, and check the log which printed by ALLHiC_plot and paste the lines with...

1. you need install python module matplotlib 2. the bin size is too large for almost all chromosomes, and the first group is too large than others, maybe you need...

You should remove HiC_scaffolds from chrn.list, and the heatmap of group1 may illustrate that the assembly of it is inappropriate. For other groups, the second parameter of the script is...