error in running gccount

[DeMagicscience]

Hi, thank you for developing Control-freec.
When I was running the gccount program, I encountered the following error message:

Unable to open fasta file for chr 248956422 in folder /home/user/reference/fasta
Please note, /home/user/reference/fasta should be a folder, not a file!

my config file for gccount was:

[general]
chrLenFile = /home/user/reference/fasta/genome.fa.fai
ploidy = 2
window = 50000
step= 10000
outputDir = /home/user/control_freec/test
chrFiles = /home/user/reference/fasta

This error message is so weird, because the reference genome can be normally used in my previous analysis, which I used WGS data of paired tumor and normal samples thus no need to calculate GC content.
Can you give me some advice how to solve this problem?
Thank you for your time!

[valeu]

It can be that the version of gccount you use does not understand the fa.fai format (while FREEC does). You can try to provide the chromosome length file in a tab-delimited format like this one: http://bioinfo-out.curie.fr/projects/freec/src/hg19.len