Out of range about fithic HOT 8 OPEN

Hi! I've encountered the same issue. Have you resolved this issue?

from fithic.

Hi, this is generally about file formatting and having wrong number of fields in one of the input files. I could help best if you paste a few of the lines from each input file.

from fithic.

I have an error while running fithic:

Command:
fithic -f 02_hicpro2fithic/fithic.fragmentMappability.gz -i 02_hicpro2fithic/fithic.interactionCounts.gz -t 02_hicpro2fithic/fithic.biases.gz -r 10000 -o 02_fithic_outputs

My input files are created by the hicpro2fithic.py of HiC-Pro_3.1.0 (version), and the output biases file (fithic.biases.gz) is blank every other line, but not in HiC-Pro_2.11.1 (versions). So I wonder if it's the version issue of subscripts (hicpro2fithic.py)?

input files: (hicpro2fithic.py of HiC-Pro_3.1.0)
zcat fithic.biases.gz | head

chr1 5000 -1

chr1 15000 -1

chr1 25000 -1

chr1 35000 -1

chr1 45000 -1

chr1 55000 -1

zcat fithic.fragmentMappability.gz | head
chr1 0 5000 0 0
chr1 10000 15000 0 0
chr1 20000 25000 0 0
chr1 30000 35000 0 0
chr1 40000 45000 0 0
chr1 50000 55000 0 0

zcat fithic.interactionCounts.gz | head
chr1 3005000 chr1 3005000 166
chr1 3005000 chr1 3015000 142
chr1 3005000 chr1 3025000 90
chr1 3005000 chr1 3035000 42
chr1 3005000 chr1 3045000 15
chr1 3005000 chr1 3055000 51

The following input files for fithic are error-free!

input files: (hicpro2fithic.py of HiC-Pro_2.11.1)
zcat fithic.biases.gz | head

chr1 5000 -1
chr1 15000 -1
chr1 25000 -1
chr1 35000 -1
chr1 45000 -1
chr1 55000 -1

So is it because of the version issue?

from fithic.

Blank lines will do it. Please remove all the blank lines and try. I will get in touch with HiCPro developers about this. Or you can post this on their github issues if you don't mind.

from fithic.

Thanks! It is error-free after removing all the blank lines, but how to avoid the blank lines in the output biases file (fithic.biases.gz) of hicpro2fithic.py from HiC-Pro_3.1.0 (python3)? That's what needs to be resolved.

from fithic.

I posted it on HiCpro github. They should take care of it soon, an extra \n in Line 87 of the script. Likely got introduced during Python 3 conversion.

from fithic.

Thanks! That's great!

from fithic.

thanks."zcat fithic.biases.gz | grep -v '^$' | gzip > fithic.biases2.gz"

from fithic.