ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/ isnt reachable

[ilkaybuysal]

Hello everyone,

The pfam database isn't reachable from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/
Would download it from somewhere else change the results? and if we can download from somewhere else which version/website do you recommend?

Thanks a lot!

[mikeraiko]

Hello!
Maybe it was just a sever downtime, it seems working, and most recent Pfam-A database is here:
ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam33.1/Pfam-A.hmm.gz

But I suggest to use our another tool, viralVerify, with the -p option to obtain more accurate results for plasmid analysis. It is provided with the database, but you may use the whole set of Pfam-A hmms as well.

[ilkaybuysal]

Thanks a lot! yes it is working now.

I'm downloading viralverify as well, thanks.

I was wondering how we specify the database? for example I'm trying to run this (on there server):
/usr/local/plasmidVerify-1.0/plasmidverify.py
-f /scratch/results/contigs.fasta -o /scratch/2020_11_16_plasmidverify_results/
--db bioinfo/hmmer/3.3.1

it doesn't accept --db bioinfo/hmmer/3.3.1, how should i provide the wanted db?

[mikeraiko]

--db is for local BLAST. To provide hmm database, use --hmm

You'll need the unpacked Pfam-A.hmm.gz - please check the link I posted above.

[ilkaybuysal]

so can we use it also with blast?

The hmm is already installed on the server though.
when i want to search hmm, then I have tried this:
/usr/local/plasmidVerify-1.0/plasmidverify.py -f /scratch/results/contigs.fasta -o /scratch/uysal/2020_11_16_plasmidverify_results/ --hmm /usr/local/hmmer-3.1b2/

2020-11-16 13:31:48
Gene prediction...
Error: File format problem in trying to open HMM file /usr/local/hmmer-3.1b2/.
File exists, but appears to be empty?

hmmsearch run failed

it is not empyth though