GeometryComponentFilter.cpp

[patidarr]

Hi,

I am getting following Error,
Could you please help me solve the issue?

library(EthSEQ)

data.dir = file.path(tempdir(),"EthSEQ_Data")
out.dir = file.path(tempdir(),"EthSEQ_Analysis")

Download BAM file used in the analysis

dir.create(data.dir)
download.file(

• "https://github.com/aromanel/EthSEQ_Data/raw/master/NA07357_only10000SNPs.bam",
• destfile = file.path(data.dir,"Sample.bam"))
  trying URL 'https://github.com/aromanel/EthSEQ_Data/raw/master/NA07357_only10000SNPs.bam'
  Content type 'application/octet-stream' length 69869713 bytes (66.6 MB)
  ==================================================
  downloaded 66.6 MB

download.file(

• "https://github.com/aromanel/EthSEQ_Data/raw/master/NA07357_only10000SNPs.bam.bai",
• destfile = file.path(data.dir,"Sample.bam.bai"))
  trying URL 'https://github.com/aromanel/EthSEQ_Data/raw/master/NA07357_only10000SNPs.bam.bai'
  Content type 'application/octet-stream' length 339928 bytes (331 KB)
  ==================================================
  downloaded 331 KB

Create BAM files list

write(file.path(data.dir,"Sample.bam"),file.path(data.dir,"BAMs_List.txt"))

Run the analysis

ethseq.Analysis(

• bam.list = file.path(data.dir,"BAMs_List.txt"),
• out.dir = out.dir,
• model.gds = "Reference_SS2_10000SNPs.gds",
• verbose=TRUE,
• aseq.path = out.dir,
• mbq=20,
• mrq=20,
• mdc=10,
• run.genotype = TRUE,
• composite.model.call.rate = 1,
• cores=1)
  [2017-04-27 07:06:08] Running EthSEQ v2.0.1
  [2017-04-27 07:06:08] Working directory: /tmp/RtmptNCImv/EthSEQ_Analysis
  [2017-04-27 07:06:08] Create /tmp/RtmptNCImv/EthSEQ_Analysis folder
  [2017-04-27 07:06:08] Create /tmp/RtmptNCImv/EthSEQ_Analysis/ASEQGenotypes/ folder
  [2017-04-27 07:06:08] Run ASEQ to generate genotypes for 1 samples
  trying URL 'https://github.com/aromanel/EthSEQ_Data/raw/master/ASEQ_binaries/linux64/ASEQ'
  Content type 'application/octet-stream' length 2091089 bytes (2.0 MB)
  ==================================================
  downloaded 2.0 MB

[2017-04-27 07:06:09] Computing pileup of BAM file /tmp/RtmptNCImv/EthSEQ_Data/Sample.bam
[2017-04-27 07:06:14] Create target model
[2017-04-27 07:06:14] Create aggregated model
[2017-04-27 07:06:16] Perform PCA on aggregated model
Principal Component Analysis (PCA) on genotypes:
Excluding 0 SNP on non-autosomes
Excluding 987 SNPs (monomorphic: TRUE, < MAF: NaN, or > missing rate: 0)
Working space: 601 samples, 9,013 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0, 1 and 2) = 1364319
Thu Apr 27 07:06:16 2017 (internal increment: 4300)
[==================================================] 100%, completed
Thu Apr 27 07:06:17 2017 Begin (eigenvalues and eigenvectors)
Thu Apr 27 07:06:17 2017 Done.
[2017-04-27 07:06:17] Infer ethnicities

R: GeometryComponentFilter.cpp:34: virtual void geos::geom::GeometryComponentFilter::filter_ro(const geos::geom::Geometry*): Assertion `0' failed.
Aborted