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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
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Error prompt on DIAMOND database #584

Open cheryllhh opened 2 years ago

cheryllhh commented 2 years ago

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 

DIAMOND/2.0.8 is loaded 
diamond v2.0.8.146 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 48
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: 
#Target sequences to report alignments for: 1
Opening the database...  [0.066s]
Error: Incomplete database file. Database building did not complete successfully.

Can anyone have any idea what went wrong?

My script is as follows:

module load DIAMOND/2.0.8
diamond blastx -b 12 -q /home/J_clean.clstr -d /home/db/virus_protein_diamond_db_v23/U-RVDBv23.0-prot -o J.prodb.diamond.match --sensitive -f 100 --salltitles -e 0.00001 --max-target-seqs 1

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

bbuchfink commented 2 years ago

Have you tried remaking the database?

cheryllhh commented 2 years ago

Yes, tried 3 times.

cheryllhh commented 2 years ago

Hi, I would like to inform you that the issue has been solved.

Fabineves7 commented 2 years ago

Hi Cherylhh,

Can you tell me how you solve the issue? I am also struggling with the same issue.

bbuchfink commented 2 years ago

Hi Cherylhh,

Can you tell me how you solve the issue? I am also struggling with the same issue.

What is your diamond version?

cheryllhh commented 2 years ago

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

cheryllhh commented 2 years ago

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: @.***>

bbuchfink commented 2 years ago

This problem has already been fixed in v2.0.9. It allows to build databases with very little memory.