https://sourceforge.net/p/provean/activity/Recent activity for proveanenTue, 14 Feb 2023 15:14:18 -0000https://sourceforge.net/p/provean/discussion/general/thread/651a057bf8/?limit=25#d8d5I 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...Andrius MerkysTue, 14 Feb 2023 15:14:18 -0000https://sourceforge.net/p/provean/discussion/general/thread/651a057bf8/?limit=25#d8d5https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2/1885/b9b7Great!Ming GaoTue, 05 Oct 2021 11:58:58 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2/1885/b9b7https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/8fd5/40f5Thank 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+.Gao GuangqiTue, 05 Oct 2021 05:16:55 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/8fd5/40f5https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2/1885Thank 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+.Gao GuangqiTue, 05 Oct 2021 05:13:54 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2/1885https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2You 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*"Ming GaoTue, 05 Oct 2021 04:36:36 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/68c2https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/8fd5Hi, 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 filesGuillem Santamaria AguilarMon, 04 Oct 2021 15:15:55 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3b/8fd5https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8f08/c24d/64eeHi, 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!Gao GuangqiSun, 03 Oct 2021 05:49:53 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8f08/c24d/64eehttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/5106Hi, 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!Gao GuangqiSun, 03 Oct 2021 05:40:48 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/5106https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3bHi, 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!Gao GuangqiSun, 03 Oct 2021 05:40:46 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467d/8d3bhttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/69a7Hi, 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...Guillem Santamaria AguilarTue, 28 Sep 2021 11:48:28 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/69a7https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467dHi, 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/ .Guillem Santamaria AguilarTue, 28 Sep 2021 10:54:00 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368/467dhttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368Hi Gullem, have you fixed this issue?Ming GaoSun, 26 Sep 2021 05:14:45 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84/c368https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8e74Hi, same here, I used provean1.1.5, latest blast and db/nr, CDHIT4.8.1. line 187; 27193 Segmentation fault ( core dumped) $COMMAND. Thanks!Ming GaoSun, 26 Sep 2021 05:13:49 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8e74https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84Hi! 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...Guillem Santamaria AguilarMon, 19 Jul 2021 12:05:55 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#fc84https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#9607I 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,Shanshan GuTue, 23 Feb 2021 11:29:45 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#9607https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5c/5e83/0c95I'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 $COMMANDDewan ShresthaTue, 30 May 2017 20:45:50 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5c/5e83/0c95https://sourceforge.net/p/provean/discussion/general/thread/9bfdf124/?limit=25#a086I have tried to compile provean 1.1.5 and 1.1.4 both with g++ 4.2.1 and g++ 4.9.2...GustavMon, 17 Nov 2014 14:01:04 -0000https://sourceforge.net/p/provean/discussion/general/thread/9bfdf124/?limit=25#a086https://sourceforge.nethttp%3A//sourceforge.net/projects/provean/files/provean-1.1.5.tar.gz/downloadproveanWed, 07 May 2014 16:39:03 -0000http://sourceforge.net/projects/provean/files/provean-1.1.5.tar.gz/downloadhttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5c/5e83Thank you for reporting the problem. Could you send me those protein sequences and...Yongwook ChoiThu, 01 May 2014 15:23:24 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5c/5e83https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8f08/c24dThank you for reporting the problem. Could you let me know which version of BLAST...Yongwook ChoiThu, 01 May 2014 15:21:16 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#8f08/c24dhttps://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=25#d857I appear to have the same problem as described by Michael Dickens. It only happens...Sebastien RenautWed, 30 Apr 2014 21:54:00 -0000https://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=25#d857https://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=25#e8caSebastien RenautWed, 30 Apr 2014 21:53:25 -0000https://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=25#e8cahttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5cI appear to have the same problem you describe. It only happens on some protein sequences....Sebastien RenautWed, 30 Apr 2014 21:53:05 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5chttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5cI appear to have the same problem you describe. It only happens on some protein sequences....Sebastien RenautWed, 30 Apr 2014 21:52:49 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=25#ba5chttps://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=50#e8caI appear to have the same problem as described by Michael Dickens. It only happens...Sebastien RenautWed, 30 Apr 2014 21:51:24 -0000https://sourceforge.net/p/provean/discussion/notice/thread/7203d182/?limit=50#e8cahttps://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=50#8f08provean version 1.1.4 (tried again with 1.1.3 and still got segmentation fault) computer...Michael DickensFri, 18 Apr 2014 17:10:07 -0000https://sourceforge.net/p/provean/discussion/general/thread/dc1e8204/?limit=50#8f08https://sourceforge.nethttp%3A//sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/downloadproveanThu, 06 Mar 2014 21:22:02 -0000http://sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/downloadproveanThu, 06 Mar 2014 20:35:09 -0000http://sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/downloadproveanWed, 05 Mar 2014 21:11:05 -0000http://sourceforge.net/projects/provean/files/provean-1.1.4.tar.gz/download