Failure to extract bases from fasta reference

[cizydorczyk]

I am getting the following error when I try several different P. aeruginosa genbank references from NCBI. I have also seen this error appearing in other people's issues on here.

[13:32:03] Running: freebayes-parallel reference/ref.txt 12 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[13:32:41] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' 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 2>> snps.log
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

[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_011770:56274-56281
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
[13:32:41] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf 2>> snps.log

Specifically, [variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_011770:56274-56281.

This error seems to result in 0 SNPs being called even when SNPs are expected.

Any ideas?

And is Snippy still being maintained?

Thank you,
Conrad