Originally posted by Petr
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I am trying to run:
Code:
cat chr3.vcf | fill-aa -a human_ancestor_3.fa.bz | gzip -c >out.sort.ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.geno types.vcf
But I am getting the following error:
[W::fai_fetch] Reference 3:60069-160069 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 3:60069-160069
The command "samtools faidx human_ancestor_3\.fa\.bz 3\:60069\-160069" returned non-zero status 256.
>3:60069-160069
at /usr/local/share/perl5/FaSlice.pm line 56.
FaSlice::throw('FaSlice=HASH(0x2227f08)', 'The command "samtools faidx h uman_ancestor_3\.fa\.bz 3\:60069...', '.\x{a}', '>3:60069-160069\x{a}') called a t /usr/local/share/perl5/FaSlice.pm line 79
FaSlice::cmd('FaSlice=HASH(0x2227f08)', 'samtools faidx human_ancestor_3 \.fa\.bz 3\:60069\-160069') called at /usr/local/share/perl5/FaSlice.pm line 125
FaSlice::read_chunk('FaSlice=HASH(0x2227f08)', 3, 60069) called at /usr/ local/share/perl5/FaSlice.pm line 153
FaSlice::get_base('FaSlice=HASH(0x2227f08)', 3, 60069) called at /usr/lo cal/bin/fill-aa line 148
main::fill_aa('HASH(0x1d52a68)', 'human_ancestor_3.fa.bz') called at /us r/local/bin/fill-aa line 18
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