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jrvalverde / DistDNA

A fast program to build a distance matrix between DNA sequences (unpublished)
GNU General Public License v3.0
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Why there is negative memory size? #2

Open xiekunwhy opened 3 years ago

xiekunwhy commented 3 years ago

Hi,

I got memory allocation error like following, why there is negative memory size?

Error: could not allocate -1281080257 bytes of memory

Best, Kun

jrvalverde commented 3 years ago

I am not sure. Can you provide more information?

That might have happened if the program is requesting too big a chunk of memory. In that case, it exceeds the size of the maximum signed integer in your machine and the numbers start looking negative. To be sure, it would help if you could provide some extra info. I beg your understanding since I wrote this program 11 years ago when we were starting work on NGS (metagenomics and bacterial evolution), and haven't revisited it since (we stopped doing NGS-based evolution around 2015).

Which program are you using (distdna, compdna)?

What size are the sequences you are using? Could it be you are trying to use distdna with an eukaryotic (plant or animal) genome?

What distance method do you want to apply?

What are the parameters?

Running the program with '-h' or '-?' will usually give you lots of useful information. If I remember well, one gave info on the program options and the other full advice on the methods, usage, selection and choices.

            j

On Wed, 30 Dec 2020 18:51:37 -0800 xiekunwhy notifications@github.com wrote:

Hi,

I got memory allocation error like following, why there is negative memory size?

Error: could not allocate -1281080257 bytes of memory

Best, Kun

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/jrvalverde/DistDNA/issues/2

-- Scientific Computing Service Centro Nacional de Biotecnología, CSIC. c/Darwin, 3. 28049 Madrid +34 91 585 45 05 +34 659 978 577

xiekunwhy commented 3 years ago

Hi, Thank for your answers. Here are some detail informations of my data.

Which program are you using (distdna, compdna)? I use "ddna: distdna.c" to calculate distance matrix. And I also want to know the differences between distdna and distdna2.

What size are the sequences you are using? Could it be you are trying to use distdna with an eukaryotic (plant or animal) genome? Yes, I use ddna for a huge human data set, with 597 individuals and about 5 millions snps. Can you do some modification to deal with such a huge dataset if the current version can not do that?

What distance method do you want to apply? I am trying to calculate uncorrected distance (p-distance?).

What are the parameters? ddna -i -o --uncorrected

Thank you again and sorry to bother you in your holiday.

Best, Kun

jrvalverde commented 3 years ago

Sorry for the delay. I've been stranded out of home due to heavy snowfalls and am slowly retaking pending matters. Will get back to you ASAP.

On Fri, 01 Jan 2021 17:10:39 -0800 xiekunwhy notifications@github.com wrote:

Hi, Thank for your answers. Here are some detail informations of my data.

Which program are you using (distdna, compdna)? I use "ddna: distdna.c" to calculate distance matrix. And I also want to know the differences between distdna and distdna2. What size are the sequences you are using? Could it be you are trying to use distdna with an eukaryotic (plant or animal) genome? Yes, I use ddna for a huge human data set, with 597 individuals and about 5 millions snps. Can you do some modification to deal with such a huge dataset if the current version can not do that?

What distance method do you want to apply? I am trying to calculate uncorrected distance (p-distance?).

What are the parameters? ddna -i -o --uncorrected

Thank you again and sorry to bother you in your holiday.

Best, Kun

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/jrvalverde/DistDNA/issues/2#issuecomment-753413120

-- Scientific Computing Service Centro Nacional de Biotecnología, CSIC. c/Darwin, 3. 28049 Madrid +34 91 585 45 05 +34 659 978 577