search

choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
185 stars 87 forks source link

Segfault when using BED file #72

Closed wiedenhoeft closed 6 years ago

wiedenhoeft commented 6 years ago

I'm using version 2.1.3.beta. I got a hg19 BED file from UCSC, however, I get a segfault:

Reading: /home/wiedenhoeft/projects/brainchild/data//hg19.bed

Segmentation fault (core dumped) Error: Execution halted

When I omit --bed, this does not happen, and scores are calculated as expected.

choishingwan commented 6 years ago

Do you mind showing me your whole log file and also head your bed file for me?

Thanks

wiedenhoeft commented 6 years ago

head data/hg19-3col.bed chr1 11873 14409 chr1 11873 14409 chr1 11873 14409 chr1 14361 16765 chr1 16857 17751 chr1 15795 18061 chr1 14361 19759 chr1 14361 19759 chr1 14361 19759 chr1 16857 19759

PRSice 2.1.3.beta (20 July 2018) https://github.com/choishingwan/PRSice (C) 2016-2017 Shing Wan (Sam) Choi, Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly GNU General Public License v3

If you use PRSice in any published work, please cite: Jack Euesden Cathryn M. Lewis Paul F. O'Reilly (2015) PRSice: Polygenic Risk Score software. Bioinformatics 31 (9): 1466-1468

2018-08-16 05:45:04 /opt/versions/PRSice/2.1.3.beta//PRSice_linux \ --A1 A1 \ --A2 A2 \ --all-score \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base /home/wiedenhoeft/projects/brainchild/data//discovery//GWAS_CP_all.txt \ --bed /home/wiedenhoeft/projects/brainchild/data//hg19-3col.bed \ --beta \ --binary-target F,F,F,F \ --bp dummy1 \ --chr dummy2 \ --feature exon,gene,protein_coding,CDS \ --lower 1e-06 \ --missing no_mean_imputation \ --model add \ --no-clump \ --no-default \ --out /home/wiedenhoeft/projects/brainchild/data/output/segfault/prsice \ --pheno-col T1_AWMA_tot,T1_Backdig_tot,T1_Threeback_corr_min_FA,T1_zravens \ --pheno-file /home/wiedenhoeft/projects/brainchild/data/output/segfault/BRAINCHILD_MASTERFILE_IID.csv \ --pvalue Pval \ --se SE \ --seed 0 \ --snp MarkerName \ --stat Beta \ --target /home/wiedenhoeft/projects/brainchild/data//karolinska//QCfinal \ --thread 150 \ --upper 1

Loading Genotype file: /home/wiedenhoeft/projects/brainchild/data//karolinska//QCfinal (bed)

76 people (35 male(s), 41 female(s)) observed 76 founder(s) included

111650 ambiguous variant(s) excluded 611666 variant(s) included

Reading: /home/wiedenhoeft/projects/brainchild/data//hg19-3col.bed

wiedenhoeft commented 6 years ago

P.S. I tried to use the full BED file (http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=686362417_RgWmtAKWaDIaBpA9aAUHoD16dvMf&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_knownGene&hgta_ctDesc=table+browser+query+on+knownGene&hgta_ctVis=pack&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbExonBases=0&fbIntronBases=0&fbDownBases=200&hgta_doGetBed=get+BED), but PRSice seems to freeze then.

choishingwan commented 6 years ago

If you don't mind, could you check the latest release and see if that solves the problem?

wiedenhoeft commented 6 years ago

Isn't 2.1.3 the latest?

choishingwan commented 6 years ago

Yes, but I also update the same build (not the best practice I know) whenever some important bug is fixed

wiedenhoeft commented 6 years ago

Agreed, that is certainly an issue with reproducibility. Isn't that what the last digit in the version number is for? ;-) But anyway, it doesn't crash anymore, thanks so much for the quick fix!