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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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error in running gccount #143

Open DeMagicscience opened 6 months ago

DeMagicscience commented 6 months ago

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 commented 4 months ago

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