provean version 1.1.4 (tried again with 1.1.3 and still got segmentation fault)
computer is 64bit with 64Gb memory
====== CD-HIT version 4.5.7 (built on Apr 17 2014) ======
provean -q ../examples/P04637.fasta -v ../examples/P04637.var -d /database/nr --psiblast /galaxy/bin/psiblast --cdhit /galaxy/bin/cd-hit --blastdbcmd /galaxy/bin/blastdbcmd
## PROVEAN v1.1 output ##
## Input Arguments ##
provean -q ../examples/P04637.fasta -v ../examples/P04637.var -d /database/nr --psiblast /galaxy/bin/psiblast --cdhit /galaxy/bin/cd-hit --blastdbcmd /galaxy/bin/blastdbcmd
## Parameters ##
# Query sequence file: ../examples/P04637.fasta
# Variation file: ../examples/P04637.var
# Protein database: /database/nr
# Supporting sequence set file (optional): Not provided
# Supporting sequence set file for storing (optional): Not provided
# Substitution matrix: BLOSUM62
# Gap costs: 10, 1
# Clustering threshold: 0.750
# Maximum number of clusters: 30
[11:34:46] loading query sequence from a FASTA file...
[11:34:46] loading variations...
[11:34:46] searching related sequences...
[11:37:49] retrieving subject sequence information...
[11:37:52] clustering subject sequences...
[11:37:52] selecting clusters...
Segmentation fault
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Thank you for reporting the problem. Could you let me know which version of BLAST you used? Have you seen the same problem for other input data? If so, could you send me the input files so that I can test it out.
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Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
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Thank you for reporting the problem. Could you send me those protein sequences and variants that caused the problem? Could you also let me know which version of BLAST and CD-HIT you had used?
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Hi! I was wondering if since this thread was started any of you found a solution to this issue. I'm trying to run PROVEAN 1.1.5 in the cluster of my institute, where I don't have admin privileges, so I did the instalation with the ./configure --prefix=/other/path/. I'm using BLAST 2.12.0 and CDHIT 4.8.1, with the latest release of NR ncbi database. I'm getting that same segmentation fault in the line 187, both with my protein set and with the example (P04637.fasta and P04637.var). If anybody had any suggestion about how to solve this it would be great, as I'm testing thousands of proteins so using the online tool is not viable.
Cheers!
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Hi,
Yes, thanks to thanks to Yongwook Choi I managed to solve it. The problem is that it doesn't work with last version of the database. I downloaded the 2011 version from ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/ .
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
The file is huge, I cannot send it to you. You need to download the files with the command:
for i in {00..48}
do
wget ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/nr.$i.tar.gz
done
And then untar the files
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Thank you very much!
As Ming Gao saying, both nr_v4 and nr_Aug_2011 can work with provean 1.1.5.
I solved the problem (Segmentation fault) with nr_v4 (https://ftp.ncbi.nlm.nih.gov/blast/db/v4/) and BLAST 2.4.0+.
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Hi,
Yes, thanks to thanks to Yongwook Choi I managed to solve it. The problem
is that it doesn't work with last version of the database. I downloaded the
2011 version from ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/ .
provean version 1.1.4 (tried again with 1.1.3 and still got segmentation fault)
computer is 64bit with 64Gb memory
====== CD-HIT version 4.5.7 (built on Apr 17 2014) ======
Thank you for reporting the problem. Could you let me know which version of BLAST you used? Have you seen the same problem for other input data? If so, could you send me the input files so that I can test it out.
Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
I appear to have the same problem you describe.
It only happens on some protein sequences.
Running provean v1.1.4
line 187: 31527 Segmentation fault (core dumped) $COMMMAND
Last edit: Sebastien Renaut 2014-04-30
Thank you for reporting the problem. Could you send me those protein sequences and variants that caused the problem? Could you also let me know which version of BLAST and CD-HIT you had used?
I'm using BLAST 2.6.0 and CDHIT 4.6.6, and when i ran the example from provean i got the following segmentation error:
[15:05:35] searching related sequences...
[15:35:19] clustering subject sequences...
/usr/local/bin/provean.sh: line 188: 90854 Segmentation fault: 11 $COMMAND
I am having the same problem here.
I'm using BLAST 2.10.1 and CDHIT 4.8.1, and i got the following segmentation error:
[18:46:17] searching related sequences...
[18:46:41] clustering subject sequences...
/picb/evolgen/users/gushanshan/software/provean/installed/bin/provean.sh: line 188: 51582 Segmentation fault $COMMAND
Could you give me some tips?
Best regards,
Hi! I was wondering if since this thread was started any of you found a solution to this issue. I'm trying to run PROVEAN 1.1.5 in the cluster of my institute, where I don't have admin privileges, so I did the instalation with the ./configure --prefix=/other/path/. I'm using BLAST 2.12.0 and CDHIT 4.8.1, with the latest release of NR ncbi database. I'm getting that same segmentation fault in the line 187, both with my protein set and with the example (P04637.fasta and P04637.var). If anybody had any suggestion about how to solve this it would be great, as I'm testing thousands of proteins so using the online tool is not viable.
Cheers!
Hi Gullem, have you fixed this issue?
Hi,
Yes, thanks to thanks to Yongwook Choi I managed to solve it. The problem is that it doesn't work with last version of the database. I downloaded the 2011 version from ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/ .
Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
Hi,
I can not open the ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/, it need user name and password? can you send the database to me (gaoguangqi@caas.cn)? Thank you very much!
Hi,
The file is huge, I cannot send it to you. You need to download the files with the command:
for i in {00..48}
do
wget ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/nr.$i.tar.gz
done
And then untar the files
Thank you very much!
As Ming Gao saying, both nr_v4 and nr_Aug_2011 can work with provean 1.1.5.
I solved the problem (Segmentation fault) with nr_v4 (https://ftp.ncbi.nlm.nih.gov/blast/db/v4/) and BLAST 2.4.0+.
You also can download V4 version from NCBI, https://ftp.ncbi.nlm.nih.gov/blast/db/v4/
Try this command:
wget --recursive -e robots=off --reject "indexl.html" --no-host-directories --cut-dirs=6 https://ftp.ncbi.nlm.nih.gov/blast/db/v4/ -A "nr_v4*"
Thank you very much! I solved the problem (Segmentation fault) with nr_v4 (https://ftp.ncbi.nlm.nih.gov/blast/db/v4/) and BLAST 2.4.0+.
Great!
Hi,
Yes, thanks to thanks to Yongwook Choi I managed to solve it. The problem
is that it doesn't work with last version of the database. I downloaded the
2011 version from ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/ .
El dom, 26 sept 2021 a las 7:14, Ming Gao (gaom001@users.sourceforge.net)
escribió:
Hi, same here, I used provean1.1.5, latest blast and db/nr, CDHIT4.8.1.
line 187; 27193 Segmentation fault ( core dumped) $COMMAND.
Thanks!