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I tried running anno on our data and it is giving the below warning messages. But output annotated vcf was generated without any issues.
Load reference genome hs37d5.fa...
DONE: 86 chromosomes and 3137454505 bases are loaded.
Load codon file codon.txt...
DONE: codon file loaded.
Load priority file priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file refFlat_hg19.nochr.txt.gz...
DONE: 39173 gene loaded.
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
DONE: Generated frequency of each annotype type in [ output.vcf.gz.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ output.vcf.gz.top.anno.frq ].
Ts/Tv ratio: 2.41531
Ts observed: 40128 times; Tv observed: 16614 times.
DONE: Generated frequency of each base change in [ output.vcf.gz.base.frq ].
DONE: Generated frequency of each codon change in [ output.vcf.gz.codon.frq ].
DONE: Generated frequency of indel length in [ output.vcf.gz.indel.frq ].
DONE: 62169 varaints are annotated.
DONE: Generated annotation output in [ output.vcf.gz ].
DONE: Indexing succeed!
Annotation succeed!
Dear anno team,
I tried running anno on our data and it is giving the below warning messages. But output annotated vcf was generated without any issues.
Load reference genome hs37d5.fa...
DONE: 86 chromosomes and 3137454505 bases are loaded.
Load codon file codon.txt...
DONE: codon file loaded.
Load priority file priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file refFlat_hg19.nochr.txt.gz...
DONE: 39173 gene loaded.
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
Cannot fread()!
DONE: Generated frequency of each annotype type in [ output.vcf.gz.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ output.vcf.gz.top.anno.frq ].
Ts/Tv ratio: 2.41531
Ts observed: 40128 times; Tv observed: 16614 times.
DONE: Generated frequency of each base change in [ output.vcf.gz.base.frq ].
DONE: Generated frequency of each codon change in [ output.vcf.gz.codon.frq ].
DONE: Generated frequency of indel length in [ output.vcf.gz.indel.frq ].
DONE: 62169 varaints are annotated.
DONE: Generated annotation output in [ output.vcf.gz ].
DONE: Indexing succeed!
Annotation succeed!
Here is the command used
anno -i test.vcf.gz -o output.vcf.gz -r hs37d5.fa -g refFlat_hg19.nochr.txt.gz -p priority.txt -c codon.txt --indexOutput
Can i ignore the above "Cannot fread" messages. Please help me to resolve this.
Thanks In Advance
Fazulur Rehaman
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