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pwwang avatar pwwang commented on June 13, 2024

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?

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plrlhb12 avatar plrlhb12 commented on June 13, 2024

It works now. The config file I downloaded before was wrong for unknown reason. Thank you so much!

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pwwang avatar pwwang commented on June 13, 2024

Great! Thanks for reporting.

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