Open cheryllhh opened 2 years ago
Have you tried remaking the database?
Yes, tried 3 times.
Hi, I would like to inform you that the issue has been solved.
Hi Cherylhh,
Can you tell me how you solve the issue? I am also struggling with the same issue.
Hi Cherylhh,
Can you tell me how you solve the issue? I am also struggling with the same issue.
What is your diamond version?
Hi Cherylhh, Can you tell me how you solve the issue? I am also struggling with the same issue.
What is your diamond version?
Sorry that I missed out on your question Fabineves7.
Hi Benjamin.
I am using DIAMOND/2.0.8 with protein database RVDB v23.
I solved it after asking my university to provide me with a custom queue on the server with 200Gb memory usage as the protein database increased from 2Gb to 10Gb. Without that, I can't even run. And the same issue will be prompted.
It will be great if it can be solved at your side rather than always having to request a special 2 weeks arrangement from the university to increase the memory size of my server. I guess there are more people seeing this issue. Currently, I had reverted back to protein database RVDB v20 using DIAMOND/2.0.8. No issue at all.
Thank you.
Cheryl
Dear Benjamin,
Yes. Tried multiple times.
Lee Hwei Huih Post-doctoral Fellow PhD (HKU), MSc (Genetics) (UKM), BSc (Industrial Biotechnology) (UNISEL) Department of Microbiology Li Ka Shing Faculty of Medicine The University of Hong Kong Room 21-026, 21/F, Block T, Queen Mary Hospital, 122 Pokfulam, Hong Kong.
From: Benjamin Buchfink @.***> Sent: 11 May 2022 18:50:18 To: bbuchfink/diamond Cc: hweihuih; Author Subject: Re: [bbuchfink/diamond] Error prompt on DIAMOND database (Issue #584)
Have you tried remaking the database?
— Reply to this email directly, view it on GitHubhttps://github.com/bbuchfink/diamond/issues/584#issuecomment-1123568212, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZDYOYJGKJ2FIRI5IQOXFZTVJOGGVANCNFSM5VUGJW7A. You are receiving this because you authored the thread.Message ID: @.***>
This problem has already been fixed in v2.0.9. It allows to build databases with very little memory.
Hi, I was previously using Diamond and did not have any problem when I updated the database. However this time I kept getting this error
Can anyone have any idea what went wrong?
My script is as follows:
I use these commands to make the U-RVDBv23.0-prot.dmnd database
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
diamond makedb --in U-RVDBv23.0-prot.fasta -d U-RVDBv23.0-prot.dmnd --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp -p 12
Thanks.
Cheryl