Closed violafanfani closed 4 years ago
Hi Viola,
how many variants are present in the file? The current version of sim1000G is not possible to load more than a few thousand variants.
Apostolos
On Thu, 17 Oct 2019 at 12:06, violafanfani notifications@github.com wrote:
Hello, I am trying to run a simulation on the chr22 and I am repeatedly getting a segmentation fault error. I am not sure if I am doing something wrong or if there is a bug somewhere.
I am running an adapted version of the script here ( https://cran.r-project.org/web/packages/sim1000G/vignettes/ExtractingRegionsForSimulation.html) using only the EUR population. The vcf file is the whole chr22 ( filtered by bcftool as described ). I am running it on a cluster on a single core with 92Gb of memory, but the same happened also with 128Gb memory and more cores.
I am fairly sure the code is working as I can run it with small region of chr22 ( as in the chr4 example you provide). The id_ped are the pedigrees of the EUR populations.
Is there anything I've missed from the documentation?
Thanks for the attention, I attach the log of the job in question.
Cheers Viola
This is the log of the job: ++++++++++++++++++
..... Parsed with column specification: cols( .default = col_character(),
#CHROM
= col_double(), POS = col_double(), QUAL = col_double() ) See spec(...) for full column specifications.caught segfault address 0x2b8d347b7220, cause 'memory not mapped'
Traceback: 1: cor(dat) 2: haplodata(haplomatrix[, polymorphic]) 3: startSimulation(vcf, subset = id_ped) An irrecoverable exception occurred. R is aborting now ... /bin/bash: line 1: 23945 Segmentation fault (core dumped) .....
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Hi Apostolos, Thank you for the quick reply. I was mistakenly using more than 300K. However I would definitively need more than 10K, do you know if that is possible? What is the limit due to? Thanks Viola
Hi Viola,
it should be possible but it will require some more computer time and memory. We haven't tested it with more than ~15000 markers.
Thanks,
Apostolos
On Fri, 18 Oct 2019 at 06:29, violafanfani notifications@github.com wrote:
Hi Apostolos, Thank you for the quick reply. I was mistakenly using more than 300K. However I would definitively need more than 10K, do you know if that is possible? What is the limit due to? Thanks Viola
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Hello, I am trying to run a simulation on the chr22 and I am repeatedly getting a segmentation fault error. I am not sure if I am doing something wrong or if there is a bug somewhere.
I am running an adapted version of the script here (https://cran.r-project.org/web/packages/sim1000G/vignettes/ExtractingRegionsForSimulation.html) using only the EUR population. The vcf file is the whole chr22 ( filtered by bcftool as described ). I am running it on a cluster on a single core with 92Gb of memory, but the same happened also with 128Gb memory and more cores.
I am fairly sure the code is working as I can run it with small region of chr22 ( as in the chr4 example you provide). The id_ped are the pedigrees of the EUR populations.
Is there anything I've missed from the documentation?
Thanks for the attention, I attach the log of the job in question.
Cheers Viola
This is the log of the job: ++++++++++++++++++