Replies: 74 comments 3 replies
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It looks like there is a problem with your R. Can you plot something to png in your R console? |
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I did capabilities and its showing png as TRUE. |
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Could you elaborate what you meant by this?
|
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I think the R plot was being made earlier but since I am using linux it was getting generated in Rplot.pdf file. I didn't notice this earlier. When you told me to check whether I am able to create plot. I did that by making basic scatter plot and the plot got generated and store in file Rplot.pdf. |
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You probably have something wrong with the "cairo" lib. Can you try to plot to png file? |
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Could you attach a screenshot running the command with the error? |
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vcfstats --vcf chr1.vcf.gz --outdir new --formula 'COUNT(1) ~ CONTIG' --title 'Number of variants on each chromosome' --config config.toml |
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Are you able to run |
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yes, I am able to run that. |
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What are the versions of the dependencies? import sys, cyvcf2, toml, pyparam, cmdy
print(sys.version)
print(cyvcf2.__version__)
print(toml.__version__)
print(pyparam.__version__)
print(cmdy.__version__) |
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I reinstalled the software. |
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Create the |
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I am able to do it. I reinstalled the software. |
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Great to hear it works for you. Feel free to reopen this issue or submit new issues if you have other questions. |
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Segmentation fault error is very likely due to |
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Yes, I am able to run it using sample.vcf provided by you. |
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Is there any way I could correct my vcf files? Any software which could format the vcf files? |
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What about this one? https://vcftools.github.io/perl_module.html#vcf-validator I myself haven't used any this kind of tools. |
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Hey, |
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vcfstats --vcf examples/sample.vcf |
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vcfstats --vcf Merged1.vcf.gz --outdir new/ --formula 'COUNT(1, group=GTTYPEs[HET,HOM]{0}) ~ CHROM' --title 'Mutant genotypes on each chromosome' --config config.toml |
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Your formula is incorrect. Try:
|
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I followed your commmand but it still showing error; |
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Let's move the conversations here: |
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@ketkijoshi278 Sorry I didn't realize that GH has this discussion mode. Let's continue the discussion here. |
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Okay. Even though I am using correct module of R which has ggplot2 package. |
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This still looks like an issue with the vcf file. Would you mind sharing the vcf file? |
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@ketkijoshi278 0.2.0 is released. Let me know if it helps in this situation. |
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Hello,
I am trying to run vcfstats.
the command:
vcfstats --vcf GEUVADIS.chr*.vcf.gz --outdir new --formula 'COUNT(1) ~ CONTIG' --title 'Number of variants on each chromosome (modified)' --config config.toml --ggs 'scale_x_discrete(name ="Chromosome",
limits=c("1","2","3","4","5","6","7","8","9","10","X")) +
ylab("# Variants")'
the error:
[2021-08-04 09:50:34,888 INFO] 1881217 variants read.
[2021-08-04 09:50:34,889 INFO] [T] Summarizing aggregations ...
[2021-08-04 09:50:34,929 INFO] [T] Composing R code ...
[2021-08-04 09:50:34,934 INFO] [T] Running R code to plot ...
[2021-08-04 09:50:34,934 INFO] [T] Data will be saved to: new/T.txt
[2021-08-04 09:50:34,934 INFO] [T] Plot will be saved to: new/T.col.png
[2021-08-04 09:50:35,631 ERROR] [T] Loading required package: ggplot2
[2021-08-04 09:50:35,632 ERROR] [T] Registered S3 methods overwritten by 'ggplot2':
[2021-08-04 09:50:35,632 ERROR] [T] method from
[2021-08-04 09:50:35,632 ERROR] [T] [.quosures rlang
[2021-08-04 09:50:35,632 ERROR] [T] c.quosures rlang
[2021-08-04 09:50:35,632 ERROR] [T] print.quosures rlang
[2021-08-04 09:50:35,632 ERROR] [T] Warning messages:
[2021-08-04 09:50:35,633 ERROR] [T] 1: In png(paste0("new/T", ".", figtype, ".png"), height = 2000, width = 2000, :
[2021-08-04 09:50:35,633 ERROR] [T] unable to load shared object '/home/kxj190026/anaconda3/envs/chip-seq/lib/R/library/grDevices/libs//cairo.so':
[2021-08-04 09:50:35,633 ERROR] [T] /home/kxj190026/anaconda3/envs/chip-seq/lib/R/library/grDevices/libs//../../../.././libharfbuzz.so.0: undefined symbol: FT_Done_MM_Var
[2021-08-04 09:50:35,633 ERROR] [T] 2: In png(paste0("new/T", ".", figtype, ".png"), height = 2000, width = 2000, :
[2021-08-04 09:50:35,633 ERROR] [T] failed to load cairo DLL
[2021-08-04 09:50:35,633 ERROR] [T] Error: unexpected input in " p = p + scale_x_discrete(name ="Chromosome", "
[2021-08-04 09:50:35,633 ERROR] [T] Execution halted
Can you please help me out with this.
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