choishingwan
commented
5 years ago That’s a known problem with 2.2.4 and I should’ve solved that in 2.2.5 (hopefully)
On Wed, 31 Jul 2019 at 12:59 AM, Li Ge notifications@github.com wrote:
Hi,
I'm running into problems even using the example commands provided by the QuickStart.
This is the command I use PRSice_linux --base TOY_BASE_GWAS.assoc \ --target TOY_TARGET_DATA \ --thread 1 \ --stat OR \ --binary-target T
`PRSice 2.2.4 (25 July 2019) https://github.com/choishingwan/PRSice (C) 2016-2019 Shing Wan (Sam) Choi and Paul F. O'Reilly GNU General Public License v3
If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019)
2019-07-30 23:57:55 PRSice_linux --A1 A1 --A2 A2 --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 --base TOY_BASE_GWAS.assoc --binary-target T --bp BP --chr CHR --clump-kb 250 --clump-p 1.000000 --clump-r2 0.100000 --interval 5e-05 --lower 5e-08 --missing MEAN_IMPUTE --model add --or --out PRSice --pvalue P --score avg --seed 142708609 --snp SNP --stat OR --target TOY_TARGET_DATA --thread 1 --upper 0.5
glibc detected PRSice_linux: malloc(): memory corruption: 0x000000000109c640 *** ======= Backtrace: ========= [0x5c2d02] [0x5c4f2d] [0x5c5b5b] [0x4ed1c8] [0x41566f] [0x409f64] [0x486231] [0x4008ad] [0x5a2a76] [0x403a15] ======= Memory map: ======== 00400000-006b1000 r-xp 00000000 00:38 31581952 ~/Software/PRSice/PRSice_linux 008b1000-008bb000 rw-p 002b1000 00:38 31581952 ~/Software/PRSice/PRSice_linux 008bb000-00946000 rw-p 00000000 00:00 0 01085000-010d0000 rw-p 00000000 00:00 0 [heap] 7ffcb3a48000-7ffcb3a69000 rw-p 00000000 00:00 0 [stack] 7ffcb3b6e000-7ffcb3b70000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped) `
Could you please help me identify the issue? Thank you very much!
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-- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC
Hi,
I'm running into problems even using the example commands provided by the QuickStart.
This is the command I use
PRSice_linux --base TOY_BASE_GWAS.assoc \ --target TOY_TARGET_DATA \ --thread 1 \ --stat OR \ --binary-target T`PRSice 2.2.4 (25 July 2019) https://github.com/choishingwan/PRSice (C) 2016-2019 Shing Wan (Sam) Choi and Paul F. O'Reilly GNU General Public License v3
If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019)
2019-07-30 23:57:55 PRSice_linux \ --A1 A1 \ --A2 A2 \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base TOY_BASE_GWAS.assoc \ --binary-target T \ --bp BP \ --chr CHR \ --clump-kb 250 \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --interval 5e-05 \ --lower 5e-08 \ --missing MEAN_IMPUTE \ --model add \ --or \ --out PRSice \ --pvalue P \ --score avg \ --seed 142708609 \ --snp SNP \ --stat OR \ --target TOY_TARGET_DATA \ --thread 1 \ --upper 0.5
glibc detected PRSice_linux: malloc(): memory corruption: 0x000000000109c640 *** ======= Backtrace: ========= [0x5c2d02] [0x5c4f2d] [0x5c5b5b] [0x4ed1c8] [0x41566f] [0x409f64] [0x486231] [0x4008ad] [0x5a2a76] [0x403a15] ======= Memory map: ======== 00400000-006b1000 r-xp 00000000 00:38 31581952 ~/Software/PRSice/PRSice_linux 008b1000-008bb000 rw-p 002b1000 00:38 31581952 ~/Software/PRSice/PRSice_linux 008bb000-00946000 rw-p 00000000 00:00 0 01085000-010d0000 rw-p 00000000 00:00 0 [heap] 7ffcb3a48000-7ffcb3a69000 rw-p 00000000 00:00 0 [stack] 7ffcb3b6e000-7ffcb3b70000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped) `
Could you please help me identify the issue? Thank you very much!