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?
3 answers
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
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.
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"
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.
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...
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.
Log in to answer this question.
-
Error "mdb_env_open: No such file or directory" on trying to execute NCBI psiblast
written by Koji •
-
Segmentation fault (core dumped) when running augustus
written by O.rka
-
Working with redundant information on BLAST output
written by flogin
-
Missing sequences in local NT database
written by Prakki Rama
-
run_BUSCO.py fails with segmentation fault with -c option
written by lakhujanivijay
-
Tophat Reporting output tracks, run out of memory, how to solve?
written by zoukai3412085 •
-
Speed up Tophat2 running
written by yuabrahamliu •
-
BUSCOs running time
written by qwzhang0601
-
"OID not found" error with GI-list and preformatted nt BLAST database
written by ziv84 •
-
Problem using a custom blast database in tblastx
written by arronar
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?
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.
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.
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.
Hi, did you find solution for this?