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poruloh / Eagle

Haplotype phasing software
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segmentation fault #17

Closed cadunesp closed 6 years ago

cadunesp commented 6 years ago

Dear Loh,

I’m very new in haplotypes analysis, and I’m trying to run Eagle v2.4. However, I get an error message:

data/frigeriodominc/software/eagle_v2.4/eagle \ --bfile=brpd11h \ --geneticMapFile=genetic_map_hg38_withX.txt.gz \ --Kpbwt=20000 \ --numThreads=16 \ --outPrefix=brpd11h

Setting number of threads to 16

=== Reading genotype data ===

Reading fam file: brpd11h.fam Total indivs in PLINK data: Nbed = 17 Total indivs stored in memory: NpreQC = 17 Reading bim file: brpd11h.bim Total snps in PLINK data: Mbed = 247 Total SNPs stored in memory: MpreQC = 247 Filling in genetic map coordinates using reference file: genetic_map_hg38_withX.txt.gz Allocating 247 x 17 bytes to temporarily store genotypes Reading genotypes and performing QC filtering on snps and indivs... Reading bed file: brpd11h.bed Expecting 1235 (+3) bytes for 17 indivs, 247 snps Filtering snp rs116807371: 0.352941 missing Filtering snp rs45554335: 0.352941 missing Filtering snp rs114069700: 0.352941 missing Filtering snp rs7921186: 0.352941 missing Filtering snp rs12217617: 0.352941 missing Filtered 247 SNPs with > 0.1 missing Filtering indiv BRPD11 BRPD11_01: 0/0 missing Filtering indiv BRPD11 BRPD11_02: 0/0 missing Filtering indiv BRPD11 BRPD11_03: 0/0 missing Filtering indiv BRPD11 BRPD11_04: 0/0 missing Filtering indiv BRPD11 BRPD11_05: 0/0 missing Filtered 17 indivs with > 0.1 missing

Total post-QC indivs: N = 0 Total post-QC SNPs: M = 0 MAF spectrum: /var/spool/slurm/slurmd/job7838725/slurm_script: line 8: 12129 Segmentation fault /data/frigeriodominc/software/eagle_v2.4/eagle --bfile=brpd11h --geneticMapFile=genetic_map_hg38_withX.txt.gz --Kpbwt=20000 --numThreads=16 --outPrefix=brpd11h

My commands are: First in PLINK/1.9: --ped .ped –map .map –make-bed

Second Eagle v2.4:

!/bin/bash

cd /data/frigeriodominc/haplo-est/split-vcf /data/frigeriodominc/software/eagle_v2.4/eagle \ --bfile=brpd11h \ --geneticMapFile=genetic_map_hg38_withX.txt.gz \ --Kpbwt=20000 \ --numThreads=16 \ --outPrefix=brpd11h

I trying to fix this problem many times but seems not working. Could you please help me and suggest some solution? I really appreciate your help. Thanks a lot Carlos

poruloh commented 6 years ago

The problem is that no SNPs or samples passed QC (due to high missingness, as indicated in the output). I will add a check in the next release to print an error message in this situation.