ytguojian
commented
6 years ago Hi, Have you resolved this eror? cheers
Open christinawu2008 opened 6 years ago
ytguojian
commented
6 years ago Hi, Have you resolved this eror? cheers
Hi there,
What does this error message mean?
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2) Hint: it is suggested to call
snpgdsOpen' to open a SNP GDS file instead ofopenfn.gds'. SNP pruning based on LD: Excluding 99,497 SNPs on non-autosomes Excluding 18,432,134 SNPs (monomorphic: TRUE, < MAF: 0.1, or > missing rate: 0.1) Working space: 107 samples, 2,877,997 SNPs using 1 (CPU) core Sliding window: 500000 basepairs, Inf SNPs |LD| threshold: 0.1 Chromosome 1: 0.02%, 372/1559630 Chromosome 2: 0.67%, 253/37734 Chromosome 3: 0.02%, 464/2070076 Chromosome 4: 0.02%, 375/1690601 Chromosome 5: 0.04%, 130/289242 Chromosome 6: 0.09%, 290/334978 Chromosome 7: 0.04%, 374/936320 Chromosome 8: 0.02%, 384/1692209 Chromosome 9: 0.02%, 46/243523 Chromosome 10: 0.02%, 517/2322820 Chromosome 11: 0.02%, 530/2163422 Chromosome 12: 0.02%, 406/1841793 Chromosome 13: 0.04%, 406/1082832 Chromosome 14: 0.02%, 365/1871957 Chromosome 15: 0.59%, 194/32634 Chromosome 16: 0.02%, 470/2171153 Chromosome 17: 0.04%, 367/969207 5943 SNPs are selected in total. /software/bioinformatics/SNPhylo-20160204/snphylo.sh: line 251: 11291 Killed "${R}" --slave --vanilla --file="${SCRIPTS_DIR}/generate_snp_sequence.R" --args -d "${gds_file}" -l "${ld_threshold}" -m "${maf_threshold}" -M "${missing_rate}" -o "${prefix_output}" -a "${num_last_autosome}"Thanks!