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