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Segmentation fault #4

Closed dongleihu closed 3 years ago

dongleihu commented 5 years ago

I was trying to use "--combine_binary_genotype_files" to combine 2 chromosomes. There are 2000 individuals and each chromosome has about 110k SNPs. I've required 100G for memory but I got an error message saying "28002 Segmentation fault". Any suggestions? Thanks.

jeffoconnell496 commented 5 years ago

Hi Donglei, I haven't used that option in several years so I don't have any immediate insight into potential problem. We can try to reproduce the problem here, but given you smallish sample size a work around would be to export the binary files to csv file, then concatenate (remove 1 header), then convert back to binary. Hope this helps, Jeff

On Mon, Apr 22, 2019 at 2:55 PM Donglei Hu notifications@github.com wrote:

I was trying to use "--combine_binary_genotype_files" to combine 2 chromosomes. There are 2000 individuals and each chromosome has about 110k SNPs. I've required 100G for memory but I got an error message saying "28002 Segmentation fault". Any suggestions? Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MMAP/MMAP-releases-issues-Q-and-A/issues/4, or mute the thread https://github.com/notifications/unsubscribe-auth/AG5VIHXE4MNDVYZ64BYBEFDPRYCZ5ANCNFSM4HHR2AXA .

dongleihu commented 5 years ago

Hi Jeff,

Thanks for the tip. I will try.

Donglei

From: jeffoconnell496 [mailto:notifications@github.com] Sent: Tuesday, April 23, 2019 7:12 AM To: MMAP/MMAP-releases-issues-Q-and-A Cc: Hu, Donglei; Author Subject: Re: [MMAP/MMAP-releases-issues-Q-and-A] Segmentation fault (#4)

Hi Donglei, I haven't used that option in several years so I don't have any immediate insight into potential problem. We can try to reproduce the problem here, but given you smallish sample size a work around would be to export the binary files to csv file, then concatenate (remove 1 header), then convert back to binary. Hope this helps, Jeff

On Mon, Apr 22, 2019 at 2:55 PM Donglei Hu notifications@github.com wrote:

I was trying to use "--combine_binary_genotype_files" to combine 2 chromosomes. There are 2000 individuals and each chromosome has about 110k SNPs. I've required 100G for memory but I got an error message saying "28002 Segmentation fault". Any suggestions? Thanks.

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