Comments (3)
I just ran that without any errors:
> vcfstats --vcf examples/sample.vcf \
--outdir examples/ \
--formula 'COUNT(1) ~ CONTIG' \
--title 'Number of variants on each chromosome' \
--config examples/config.toml
[09/28/20 22:39:24] INFO Combining regions, remind that regions should not be overlapping ...
INFO Getting vcf handler by given regions ...
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
INFO Getting instances ...
INFO INSTANCE: 'Number of variants on each chromosome'
INFO [Number of variants on each chromosome] Parsing formulas ...
INFO [Number of variants on each chromosome] plot type: col
INFO Start reading variants ...
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'X' is not defined in the header. (Quick workaround: index the file with tabix.)
INFO 105 variants read.
INFO [Number of variants on each chromosome] Summarizing aggregations ...
INFO [Number of variants on each chromosome] Composing R code ...
INFO [Number of variants on each chromosome] Running R code to plot ...
INFO [Number of variants on each chromosome] Data will be saved to: examples/Number_of_variants_on_each_chromosome.txt
INFO [Number of variants on each chromosome] Plot will be saved to: examples/Number_of_variants_on_each_chromosome.col.png
It's weird that we don't have !
in examples/config.toml
. This is how it should look like:
# generate smaller figures for demonstration
devpars = { width = 600, height = 600, res = 100}
How about yours?
from vcfstats.
It works now. The config file I downloaded before was wrong for unknown reason. Thank you so much!
from vcfstats.
Great! Thanks for reporting.
from vcfstats.
Related Issues (19)
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