vcf_parse header fail

[cmkobel]

I just installed a fresh version of snippy on linux with conda, I get the following error in snps.log when I'm calling with reads:

### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf

[W::vcf_parse] INFO 'A' is not defined in the header, assuming Type=String
Encountered an error, cannot proceed. Please check the error output above.
If feeling adventurous, use the --force option. (At your own risk!)

I don't get the error when I use contigs.

Has anybody observed something alike? Kind regards, Carl

[esteinig]

Different issue with bcftools after fresh Conda installation in contig and read inputs

[02:25:53] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' FNQ-8.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/R$
normalize v0.5

options:     input VCF file                                  -
         [o] output VCF file                                 -
         [w] sorting window size                             10000
         [n] no fail on reference inconsistency for non SNPs false
         [q] quiet                                           false
         [d] debug                                           false
         [r] reference FASTA file                            reference/ref.fa

[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)
[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_017338.1:81590-81605
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file

I tried downgrading to bcftools v10.0, v10.1, v10.2 from the Bioconda repository but all fail with the same error

Same on downgrading on a fresh install of Snippy v4.5.1

Files and reference used are test ones that worked for Snippy v4.6.0

[esteinig]

So the [fai_fetch_seq] was actually a problem with the version of vt - for some reason it got downgraded in my environment.

Check version of vt in current environment:

conda list | grep "vt"

Upgrade to correct version with:

conda install -c conda-forge -c bioconda vt=0.57721

@cmkobel wondering if the cause of your error is the same (as it occurs in same line)