Error [E::bgzf_read_block] Invalid BGZF header at offset 85619

[IPriscilla]

Dear Giulio,

When I run this command from the Mocha page on my data:

bcftools isec --no-version -Ou --complement --exclude "N_ALT>1" --write 1 $dir/$pfx.unphased.bcf $dir/$pfx.xcl.bcf | \
  bcftools annotate --no-version -Ou --remove ID,QUAL,INFO,^FMT/GT  | \
  bcftools +scatter --no-version -Ob --output $dir --scatter $(echo {{1..22},X} | tr ' ' ',') --prefix $pfx

I get these errors:

[E::bgzf_read_block] Invalid BGZF header at offset 85619
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 102544
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 102544
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 119330
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 134975
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 134975
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 152196
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 152196
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 169203
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 169203
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 185200
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 185200
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 201927
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 201927
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 201927
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 218412
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 218412
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes

We use genome build 37 for our project and the previous steps succeeded without errors.

Do you know why I get this error?

Kind regards, Priscilla

[freeseek]

These are errors from the bgzf.c file so most likely your input files are malformed. Maybe try to re-index them again. What version of BCFtools/HTSlib/MoChA are you using?