Exec format error: bcftools failing to open an indexed VCF file

Question

[Ella]

Hello,

From a VCF file, I am trying to pull the GT information (in the format of 0/1, 0/0, 2/0 etc.) for certain positions per chromosome per sample. When I run the following code I get the resulting line for each chromosome and contig:

bcftools query -t 4:58000000-59000000 -f '[ %GT]\n' myfile.vcf

[W::vcf_parse] Contig 'scaffold_869' is not defined in the header.
(Quick workaround: index the file with tabix.)

So I zip compressed and indexed the file with bgzip and tabix:

bgzip myfile.vcf 
tabix myfile.vcf.gz

When I re-run the above query with the new indexed file, I get:

bcftools query -t 4:58000000-59000000 -f '[ %GT]\n' myfile.vcf.gz.tbi
[E::hts_hopen] Failed to open file myfile.vcf.gz.tbi
[E::hts_open_format] Failed to open file "myfile.vcf.gz.tbi" : Exec
format error    Failed to read from myfile.vcf.gz.tbi: Exec format error

I have checked and changed the myfile.vcf.gz.tbi permissions to -rwxrwxrwx via chmod. I have checked the file format via htsfile and get:

myfile.vcf.gz.tbi:        Tabix compressed index data 

Also, the input VCF data is position sorted. I am using samtools version 1.10-98 and htslib 1.10.2-135 on a university server.

Can someone please suggest what is going wrong and why my file cannot be read?

Thanks in advance

Answer 1

[Pierre Lindenbaum]

not

bcftools query -t 4:58000000-59000000 -f '[ %GT]\n' indexed.vcf.gz.tbi

but

bcftools query -r 4:58000000-59000000 -f '[ %GT]\n' indexed.vcf.gz

[W::vcf_parse] Contig 'scaffold_869' is not defined in the header. (Quick workaround: index the file with tabix.)

means that there is a chromosome named scaffold_869 but it is not defined in the header (lines starting with #contig )

[Ella]

Hi Pierre, Thanks for your help. I have added the chromosome lengths into the header using:

> $ awk '/^#CHROM/ {printf("##contig=<ID=chr1,length=263206000>\n##contig=<ID=chr2,length=347119000>\n##contig=<ID=chr3,length=309664000>\n##contig=<ID=chr4,length=340129330>\n##contig=<ID=chr5,length=275007000>\n##contig=<ID=chr6,length=214272000>\n##contig=<ID=chr7,length=255482000>\n");} {print;}' file.vcf > file_header.vcf

after compressing and indexing the file_header.vcf like previously, i still get an Exec error message:

 bcftools query -r 4:58000000-59000000 -f '[ %GT]\n' file_header.vcf.gz.tbi 

[E::hts_hopen] Failed to open file file_header.vcf.gz.tbi [E::hts_open_format] Failed to open file "file_header.vcf.gz.tbi" : Exec format error Failed to read from file_header.vcf.gz.tbi: Exec format error

I have full permissions and am using samtools 1.10-98-gfaab8b0 + htslib 1.10.2-135-gf4f7f24. Any other suggestions on why samtools cant read my file?