PROVEAN not working

Question

[AnnaW]

Hello All,

I'm having troubles making PROVEAN work.

I’m getting this error while trying to run PROVEAN

Protein database:

/gpfs01/home/x/NCBI-BLAST/blastdb/ftp.ncbi.nih.gov/blast/db/nr

[17:44:08] searching related sequences...

[18:45:32] clustering subject sequences... ./provean.sh: line 187: 41879 Segmentation fault $COMMAND

Any idea what I'm doing wrong?

[Joe]

Segfaults are usually an out-of-memory issue.

How big is your dataset, how much RAM do you have available? Does the command complete successfully for minimal, or even single input data?

[biostarter]

I am having the same problem here testing on the sample data. Using top, I find that Provean is not using a 10th of my available RAM, so there must be something else wrong. Do the developers of Provean have a way to raise issues with them? I can't find any details for raising an issue online.

[Joe]

There's a web contact form: http://provean.jcvi.org/contact.php

I'd try that first, but I wouldn't expect a speedy reply.

[biostarter]

Ya I tried all those links. None of the emails work. The email I sent were not delivered. The online form you referenced did not work as well.

[shanshangu722]

Hi, did you find solution for this?

Answer 1

[AnnaW]

I ended up using PROVEAN web interface.

It seems that this segmentation fault is a common problem. I've tried using a big memory machine (500GB) but the error was still appearing. Similarly, I've tried installation via conda as well. I ended up with the same error

Answer 2

[shanshangu722]

You can try using the following versions: - BLAST+ v2.4: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.4.0/ - NR: ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/ It works for me.

[YuFeng]

Hi, do you have a backup of this nr database? I tried this link but it does not work.

Answer 3

[YuFeng]

The blast+ v2.4.0 and nr database version4 from https://ftp.ncbi.nlm.nih.gov/blast/db/v4/ works. It seems that provean does not compatible with the latest blast database (version 5).

The configuration in my provean.sh is:

BLAST_DB="/data/Database/nr_v4/nr"

PSIBLAST="/home/Software/ncbi-blast-2.4.0+/bin/psiblast"

CD_HIT="/home/Software/miniconda3/bin/cd-hit"

BLASTDBCMD="/home/Software/ncbi-blast-2.4.0+/bin/blastdbcmd"

[gaom001]

Hi YuFeng, I have some issue with V4 db download. Could you please let me know how you did it, I saw you have similar question before, but you fixed. Thnaks,

 Perl path/ncbi-blast-2.4.0+/bin/update_blastdb.pl --passive --decompress nr

Can't locate Archive/Tar.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/gaom4/proVean/ncbi-blast-2.4.0+/bin/update_blastdb.pl line 42.

[gaom001]

HI guys, I am working on proVean this week, and met all the issued people posted online. Main problems I think are elated to the versions for blast, db and cd-hit since all three get updated but probbaly not apply properly for proVean. I will going to try V4 version, as Yufeng mentioned this morning, but met new issues again.

If anyone can give me some solutions, will save me life. ...lol...

[YuFeng]

I just downloaded all tarballs from https://ftp.ncbi.nlm.nih.gov/blast/db/v4/ (nr_v4.*.tar.gz) and unzipped them (using command tar zxvf ), and it works.