MyDB.acx file is empty while make database

[sammywinchester19]

Hi,

I am trying to run this program while generating the database I have a fasta file with a bacterial genome. I tried to make .edx file and .acx file but the .acx file comes out empty, and the output alignment file which I get afterward with the next script is also empty even though I expect to see some alignments.

Suleman

[GabeAl]

Hi, A C program cannot be executed like a script. It is not like python or perl. You will need to grab the binary executable from the release page ( https://github.com/knights-lab/BURST/releases/tag/v1.0 ), not the source code. Thanks, Gabe

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On Tue, Sep 29, 2020 at 8:29 AM sammywinchester19 ***@***.***> wrote: Hi, I am trying to run this program, I changed the burst.c file to executable but still its does not preceed. Suleman — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#30>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5NOBV3CEDA6JRDNUSONZDSIHHLNANCNFSM4R5XQPXA> .

[GabeAl]

Hi, looks like you completely changed your issue (next time, please close the existing issue and open a new one, because I am emailed these issues directly and am not notified when they change).

If your acx file is empty, most likely BURST reported an issue when running. There is no way I can tell you what happened without seeing what BURST said was wrong.

Most likely you don't have enough memory. :) You will need around 6x the size of the original FASTA as RAM when building a database. To reduce this, use -d DNA QUICK 500 and -s 1000 on the commandline while building.

If you're using burst12 and are building a small amplicon DB, it can run fine on a laptop.

Otherwsie, BURST (burst15, whole-genome shotgun metagenomics) is not meant to be run on laptops or personal computers, but large workstations or servers with >128GB RAM.