Unknown file type error when running bcftools command
Hi all,
I've been trying to run this command:
bcftools view --threads 40 --samples-file /home/j/jle/jasminl/scratch/analysis/ID.txt -Oz -o /home/j/jle/jasminl/scratch/analysis/JC.vcf.gz
Where ID.txt is a file containing the ID I want to use to extract samples from the JC.vcf.gz file. However, I have been running into this error:
Failed to open -: unknown file type
Is this a common problem? What might be causing it?
Thank you.
1 answer
You haven't specified an actual input file because it's treating /home/j/jle/jasminl/scratch/analysis/JC.vcf.gz as the output file as it follows the -o flag.
It should be something like this:
bcftools view \
--threads 40 \
--samples-file /home/j/jle/jasminl/scratch/analysis/ID.txt \
-O z \
-o /home/j/jle/jasminl/scratch/analysis/JC.output.vcf.gz \
/home/j/jle/jasminl/scratch/analysis/JC.vcf.gz
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what's the version of bcftools ? otherwise I suspect there is a invisible character somewhere in your command. You shoud re-write it from scractch .
I tried rewriting it from scratch, but the same is occurring. The modules I have currently loaded onto my shell script is:
module load gcc/8.3.0 module load bcftools/1.8 module load samtools/1.13
Please let me know your thoughts, thank you.
run
bcftools viewonly, look at the available options and look if this old version of bcftools contains the options you wanted.