provean Activity
Predicting the functional effect of protein sequence variations
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Activity for provean
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Andrius Merkys posted a comment on discussion General Discussion
I am using provean v1.1.5 without the supporting set and it always fails with the following (timestamps removed): [...] retrieving subject sequence information... [...] Parsing Error I have inspected the raw blast_out file and it seems fine: there are lines containing database IDs. Then I looked into the code in src/SequenceDB.cpp, in SequenceDB::SetSequenceInfoFromBlastOut(), and I do not quite get the following line: gi = strtok(NULL, "\t\n"); I may not know C/C++ well, but it seems to me that...
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Ming Gao posted a comment on discussion General Discussion
Great!
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Gao Guangqi posted a comment on discussion General Discussion
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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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+.
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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*"
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Guillem Santamaria Aguilar posted a comment on discussion General Discussion
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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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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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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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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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 Gullem, have you fixed this issue? segmentation fault https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368 Sent from sourceforge.net because you indicated...
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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/ .
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Hi Gullem, have you fixed this issue?
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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!
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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...
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Shanshan Gu posted a comment on discussion General Discussion
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,
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Dewan Shrestha posted a comment on discussion General Discussion
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
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Gustav posted a comment on discussion General Discussion
I have tried to compile provean 1.1.5 and 1.1.4 both with g++ 4.2.1 and g++ 4.9.2...
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provean released /provean-1.1.5.tar.gz
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Yongwook Choi posted a comment on discussion General Discussion
Thank you for reporting the problem. Could you send me those protein sequences and...
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Thank you for reporting the problem. Could you let me know which version of BLAST...
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Sebastien Renaut posted a comment on discussion Notice
I appear to have the same problem as described by Michael Dickens. It only happens...
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I appear to have the same problem you describe. It only happens on some protein sequences....
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I appear to have the same problem you describe. It only happens on some protein sequences....
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I appear to have the same problem as described by Michael Dickens. It only happens...
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Michael Dickens posted a comment on discussion General Discussion
provean version 1.1.4 (tried again with 1.1.3 and still got segmentation fault) computer...
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