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2.0.1 docker version output xlsx with no annotation #79

Description

@nswh

The output of xlsx file left with the below columns empty:

ANTICODON
GENE
GENE BIOTYPE
PHYLOTREE MUT
PHYLOTREE HAPLOTYPE
MGRB FILTER
MGRB AN
MGRB AC
MGRB FREQUENCY
MITOMAP DISEASE AC
MITOMAP DISEASE AF
MITOMAP DISEASE AACHANGE
MITOMAP DISEASE HOMOPLASMY
MITOMAP DISEASE HETEROPLASMY
MITOMAP DISEASE PUBMED IDS
MITOMAP DISEASE DISEASE
MITOMAP DISEASE DISEASE STATUS
MITOMAP DISEASE HGFL
MITOMAP CONFIRMED MUTATIONS LOCUS
MITOMAP CONFIRMED MUTATIONS LOCUSTYPE
MITOMAP CONFIRMED MUTATIONS ASSOCIATEDDISEASE
MITOMAP CONFIRMED MUTATIONS ALLELE
MITOMAP CONFIRMED MUTATIONS AMINOACIDCHANGE
MITOMAP CONFIRMED MUTATIONS STATUSMITOMAPCLINGEN
MITOMAP CONFIRMED MUTATIONS LASTUPDATE
MITOMAP MUTATIONS CODING CONTROL LOCUS
MITOMAP MUTATIONS CODING CONTROL ALLELE
MITOMAP MUTATIONS CODING CONTROL DISEASE
MITOMAP MUTATIONS CODING CONTROL NUCLEOTIDECHANGE
MITOMAP MUTATIONS CODING CONTROL AMINOACIDCHANGE
MITOMAP MUTATIONS CODING CONTROL PLASMY
MITOMAP MUTATIONS CODING CONTROL STATUS
MITOMAP MUTATIONS CODING CONTROL GB FREQ
MITOMAP MUTATIONS CODING CONTROL GB SEQS
MITOMAP MUTATIONS CODING CONTROL REFERENCES
MITOMAP MUTATIONS RNA LOCUS
MITOMAP MUTATIONS RNA DISEASE
MITOMAP MUTATIONS RNA ALLELE
MITOMAP MUTATIONS RNA RNA
MITOMAP MUTATIONS RNA HOMOPLASMY
MITOMAP MUTATIONS RNA HETEROPLASMY
MITOMAP MUTATIONS RNA STATUS
MITOMAP MUTATIONS RNA MITOTIP
MITOMAP MUTATIONS RNA GB FREQ
MITOMAP MUTATIONS RNA GB SEQS
MITOMAP MUTATIONS RNA REFERENCES
MITOMAP POLYMORPHISMS AC
MITOMAP POLYMORPHISMS AF
MITOMAP POLYMORPHISMS HGFL
MITOMAP VARIANTS CODING LOCUS
MITOMAP VARIANTS CODING NUCLEOTIDECHANGE
MITOMAP VARIANTS CODING CODONNUMBER
MITOMAP VARIANTS CODING CODONPOSITION
MITOMAP VARIANTS CODING AMINOACIDCHANGE
MITOMAP VARIANTS CODING GB FREQ
MITOMAP VARIANTS CODING GB SEQS
MITOMAP VARIANTS CODING CURATEDREFERENCES
MITOMAP VARIANTS CONTROL LOCUS
MITOMAP VARIANTS CONTROL NUCLEOTIDECHANGE
MITOMAP VARIANTS CONTROL GB FREQ
MITOMAP VARIANTS CONTROL GB SEQS
MITOMAP VARIANTS CONTROL CURATEDREFERENCES
MITOTIP SCORE
MITOTIP PERCENTILE
MITOTIP QUARTILE
MITOTIP SCORE INTERPRETATION
MITOMAP STATUS
COUNT
PERCENTAGE

The script I ran is:

docker run --rm -t -v $(pwd):/home drmjc/mity:2.0.1 runall --reference hg38 --prefix $filename --min-alternate-fraction 0 --output-dir mity --min_vaf 0 $bam

screen response is:

mity version 2.0.1
Calling mitochondrial variants
Running FreeBayes in sensitive mode

> gsort version 0.1.4

mity 2.0.1
Generating mity report
sheet_name: $filename.normalise was too long and was automatically shortened

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