From pmj.dupuis at gmail.com Tue Mar 18 10:48:07 2014 From: pmj.dupuis at gmail.com (Pierre Dupuis) Date: Tue, 18 Mar 2014 10:48:07 +0100 Subject: [Inparanoid] Inparanoid server down Message-ID: Hi, I'm using inParanoid to retrieve orthologs in a cytoscape app and my program crash when trying to access inParanoid. When I try to load http://inparanoid.sbc.su.se/ in a browser, I get a 503 (Service Temporarily Unavailable) error. Is there a problem with the server ? Do you think inParanoid will be down for long ? Thanks in advance for your help. Respectfully, Pierre Dupuis. -- DUPUIS Pierre Master 2 G?nie Physiologique, Biotechnologique et Informatique, Sp?cialit? Bioinformatique & Biotechnologies, Sciences Fondamentales & Appliqu?es - Universit? de Poitiers *Tel :* +33 (0)6 83 96 91 57 *Mail :* pmj.dupuis at gmail.com *Skype* : pirdupuis Voir mon profil LinkedIn Voir mon profil Viadeo -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Tue Mar 18 18:40:44 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 18 Mar 2014 18:40:44 +0100 Subject: [Inparanoid] Inparanoid server down In-Reply-To: <59b045020775499fb6a559594c0400c1@EBOX-PROD-SRV01.win.su.se> References: <59b045020775499fb6a559594c0400c1@EBOX-PROD-SRV01.win.su.se> Message-ID: <5328851C.4010905@scilifelab.se> Dear Pierre, Apologies, but we are having some stability problems. It is up now but it may go down again. The stability problems seem related to somebody making hundreds of simultaneous accesses (sessions) to the server, which brings it down - is that what you are doing? If this is so, it would help if you could limit your usage. Bests Erik Sonnhammer On 2014-03-18 10:48, Pierre Dupuis wrote: > > Hi, > > I'm using inParanoid to retrieve orthologs in a cytoscape app and > my program crash when trying to access inParanoid. > > When I try to load http://inparanoid.sbc.su.se/ in a browser, I get > a 503 (Service Temporarily Unavailable) error. > > Is there a problem with the server ? Do you think inParanoid will > be down for long ? > > Thanks in advance for your help. > Respectfully, > Pierre Dupuis. > > > -- > DUPUIS Pierre > > Master 2 G?nie Physiologique, Biotechnologique et Informatique, > Sp?cialit? Bioinformatique & Biotechnologies, > Sciences Fondamentales & Appliqu?es - Universit? de Poitiers > > > _Tel :_ +33 (0)6 83 96 91 57 > _Mail :_ pmj.dupuis at gmail.com > _Skype_ : pirdupuis > > Voir mon profil LinkedIn > > Voir mon profil Viadeo > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Wed Mar 19 08:38:52 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Wed, 19 Mar 2014 08:38:52 +0100 Subject: [Inparanoid] Inparanoid server down In-Reply-To: References: <59b045020775499fb6a559594c0400c1@EBOX-PROD-SRV01.win.su.se> <5328851C.4010905@scilifelab.se> Message-ID: <5329498C.7090505@scilifelab.se> Dear Pierre, Thanks, yes it is very important to not start new requests before old ones are completed, as this may fill up the system and bring it down. The system seems stable now, so I hope this was the problem. PS. If you become member of the InParanoid mailling list, https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se, you can post mail to it without waiting for approval. Bests /Erik On 2014-03-18 21:55, Pierre Dupuis wrote: > > Dear Erik, > > Thank you for your response. If we are not the cause of your > problem, we are probably a part of it. > > First, we will drastically limit our usage by dropping unsucessful > requests instead of relaunching them. We are currently thinking about > an alternative solution by loading orthoXML in advance and so remove > web request. > > We are truely sorry for the inconvenience. > > Respectfully, > Pierre. > > > 2014-03-18 18:40 GMT+01:00 Erik Sonnhammer > >: > > Dear Pierre, > > Apologies, but we are having some stability problems. It is up now > but it may go down again. > > The stability problems seem related to somebody making hundreds of > simultaneous accesses (sessions) to the server, which brings it > down - is that what you are doing? If this is so, it would help > if you could limit your usage. > > Bests > Erik Sonnhammer > > On 2014-03-18 10:48, Pierre Dupuis wrote: >> >> Hi, >> >> I'm using inParanoid to retrieve orthologs in a cytoscape app >> and my program crash when trying to access inParanoid. >> >> When I try to load http://inparanoid.sbc.su.se/ in a browser, >> I get a 503 (Service Temporarily Unavailable) error. >> >> Is there a problem with the server ? Do you think inParanoid >> will be down for long ? >> >> Thanks in advance for your help. >> Respectfully, >> Pierre Dupuis. >> >> >> -- >> DUPUIS Pierre >> >> Master 2 G?nie Physiologique, Biotechnologique et Informatique, >> Sp?cialit? Bioinformatique & Biotechnologies, >> Sciences Fondamentales & Appliqu?es - Universit? de Poitiers >> >> >> _Tel :_ +33 (0)6 83 96 91 57 >> _Mail :_ pmj.dupuis at gmail.com >> _Skype_ : pirdupuis >> >> Voir mon profil LinkedIn >> >> Voir mon profil Viadeo >> >> > > > > > -- > DUPUIS Pierre > > Master 2 G?nie Physiologique, Biotechnologique et Informatique, > Sp?cialit? Bioinformatique & Biotechnologies, > Sciences Fondamentales & Appliqu?es - Universit? de Poitiers > > > _Tel :_ +33 (0)6 83 96 91 57 > _Mail :_ pmj.dupuis at gmail.com > _Skype_ : pirdupuis > > Voir mon profil LinkedIn > > Voir mon profil Viadeo > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xmaswang26 at gmail.com Thu Mar 27 05:50:28 2014 From: xmaswang26 at gmail.com (Xuan Wang) Date: Thu, 27 Mar 2014 12:50:28 +0800 Subject: [Inparanoid] A bug report for inparanoid4.1 Message-ID: Hi, developers! First of all, thank you very much for developing the user-friendly ortholog find program. I used the stand alone inparanoid in many cases. Recently, I used it on a HPC? but a bug appeared. The system info: $ cat /proc/version Linux version 2.6.32-279.el6.x86_64 (mockbuild at c6b9.bsys.dev.centos.org) (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Fri Jun 22 12:19:21 UTC 2012 $ lsb_release -a LSB Version: :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.3 (Final) Release: 6.3 Codename: Final ################################### First try: $ /usr/bin/java -version java version "1.6.0_24" OpenJDK Runtime Environment (IcedTea6 1.11.1) (rhel-1.45.1.11.1.el6-x86_64) OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode) ERRs like this: *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa3000ae70 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa30007f40 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa30014f00 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa3000afe0 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa30007f40 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa3000b080 *** *** glibc detected *** java: double free or corruption (fasttop): 0x00002baa3001e5e0 *** *** glibc detected *** java: double free or corruption (out): 0x00002baa3001b5e0 *** sh: line 1: 6311 Aborted (core dumped) java -jar seqstat.jar -m BLOSUM80 -n 1000 -i 237.faa > 237.bs Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. sh: line 1: 6374 Aborted (core dumped) java -jar seqstat.jar -m BLOSUM80 -n 1000 -i 589.faa > 589.bs Second try: $ my_java/java -version java version "1.7.0_51" Java(TM) SE Runtime Environment (build 1.7.0_51-b13) Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode) The same ERR as first try. Third try: $ my_java_32/java -version java version "1.7.0_51" Java(TM) SE Runtime Environment (build 1.7.0_51-b13) Java HotSpot(TM) Server VM (build 24.51-b03, mixed mode) Under the 32 bit java environment, no error reports. ##################### Because I have to use 64bit java for other big ram programs, it's not convenient for me to change the shell env frequently. Also, I don't know if the bug will affect the calculating results(I dug some infos on the net. A explanation is that the jar used free() twice to access a same RAM address, so when glibc checked, it was considered as a fatal error), I hope you can check the java src and help me solve the problem in 64bit java and CentOS environment. Looking forward to your early reply :) Xuan Wang -- Xuan Wang Biology, Cuiying Honors College, Lanzhou University, China Kunming institute of zoology, CAS Email: xmaswang26 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jean.nicolas.audet at gmail.com Thu Mar 27 13:41:29 2014 From: jean.nicolas.audet at gmail.com (Jean-Nicolas Audet) Date: Thu, 27 Mar 2014 08:41:29 -0400 Subject: [Inparanoid] InParanoid v4.1 does not work on more than 10000 sequences Message-ID: <006d01cf49b9$e1285d10$a3791730$@gmail.com> Hello, I've been trying to make InParanoid work using de novo transcriptomes of two non-model species (birds) I assembled with Trinity. They were 'translated' to protein sequences using Transdecoder. The resulting fasta file I'm trying to use in InParanoid looks like this (~30 000 seqs): >comp100291_c0_seq1 LPKKILLPIQQVLGHLLLALSYRGKVMQVKALKSKHEHNGPETLDAFLSSKLVVVKQPRE QAGFPLSIVFIPGEGRQERFLLHGEYNQSFCKEPVMELPRQ >comp102162_c0_seq1 PNMTLHFLKSSPGSWRLSGLVLIPYVTETISGSCETLTRLQMPAHIQQSRWKAKHGPRIL LLGLLQNLRSLFPLKVLPPGANSQLKRNCSFTSVCLIGTFYVESS >comp102206_c0_seq1 CQEQKWQKGNREEKGWAGVTVWGAYFPYLLIRCPNHQTSTPLSIHSQQHFMLCIIICPFS WLKPPVKTTQMFKGFFFKSGLKKFLALFLISWAAFATDRPLLGKQQSR I tried the example fasta files supplied with the program (called SC and EC) and it works, but when I use my files, it's stuck at the first step and it does not create any file (nor disk usage) after days. Here is what I get with my fasta files: Loading module bio/ncbi-blast-2.2.22. Formatting BLAST databases Done formatting Starting BLAST searches... Starting first BLAST pass for bf - bf on [blastall] WARNING: the -C 3 argument is currently experimental It then stays like this forever (I tried up to 6 days with 24 CPUs and 256G). I also tried supplying my Blast results (inter-sample) generated myself that I parsed with their supplied parser but then it still stays forever at the same state, again without generating any file: Done BLAST searches. Starting ortholog detection... I tried with and without bootstraping, multitreading (-a16 option) or not, as I said with or without supplied blast results and I also cleaned my fasta files for any weird characters (removed annotations, all ' * ', spaces, empty lines and dots. Now I'm running out of ideas... I'm using a Unix cluster. I tried these jobs using up to 4 to 24 CPUs with 8 to 256G memory. Finally, since it was working with SC and EC, I tried with a small subset of my transcriptomes (a few thousands sequences) and it worked. Thus it seems to me that the problem could be that InParanoid cannot take more than, say, 10000 sequences. I could split my transcriptomes into several smaller files of specified sequence ranges but then the orthologs that do not have the exact same length will have a chance to be missed if they are in two different split files. Thanks in advance for your help, Jean-Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From jean-nicolas.audet at mail.mcgill.ca Thu Mar 27 13:59:04 2014 From: jean-nicolas.audet at mail.mcgill.ca (Jean-Nicolas Audet, Mr) Date: Thu, 27 Mar 2014 12:59:04 +0000 Subject: [Inparanoid] InParanoid v4.1 does not work on more than 10000 sequences Message-ID: Hello, I've been trying to make InParanoid work using de novo transcriptomes of two non-model species (birds) I assembled with Trinity. They were 'translated' to protein sequences using Transdecoder. The resulting fasta file I'm trying to use in InParanoid looks like this (~30 000 seqs): >comp100291_c0_seq1 LPKKILLPIQQVLGHLLLALSYRGKVMQVKALKSKHEHNGPETLDAFLSSKLVVVKQPRE QAGFPLSIVFIPGEGRQERFLLHGEYNQSFCKEPVMELPRQ >comp102162_c0_seq1 PNMTLHFLKSSPGSWRLSGLVLIPYVTETISGSCETLTRLQMPAHIQQSRWKAKHGPRIL LLGLLQNLRSLFPLKVLPPGANSQLKRNCSFTSVCLIGTFYVESS >comp102206_c0_seq1 CQEQKWQKGNREEKGWAGVTVWGAYFPYLLIRCPNHQTSTPLSIHSQQHFMLCIIICPFS WLKPPVKTTQMFKGFFFKSGLKKFLALFLISWAAFATDRPLLGKQQSR I tried the example fasta files supplied with the program (called SC and EC) and it works, but when I use my files, it's stuck at the first step and it does not create any file (nor disk usage) after days. Here is what I get with my fasta files: Loading module bio/ncbi-blast-2.2.22. Formatting BLAST databases Done formatting Starting BLAST searches... Starting first BLAST pass for bf - bf on [blastall] WARNING: the -C 3 argument is currently experimental It then stays like this forever (I tried up to 6 days with 24 CPUs and 256G). I also tried supplying my Blast results (inter-sample) generated myself that I parsed with their supplied parser but then it still stays forever at the same state, again without generating any file: Done BLAST searches. Starting ortholog detection... I tried with and without bootstraping, multitreading (-a16 option) or not, as I said with or without supplied blast results and I also cleaned my fasta files for any weird characters (removed annotations, all ' * ', spaces, empty lines and dots. Now I'm running out of ideas... I'm using a Unix cluster. I tried these jobs using up to 4 to 24 CPUs with 8 to 256G memory. Finally, since it was working with SC and EC, I tried with a small subset of my transcriptomes (a few thousands sequences) and it worked. Thus it seems to me that the problem could be that InParanoid cannot take more than, say, 10000 sequences. I could split my transcriptomes into several smaller files of specified sequence ranges but then the orthologs that do not have the exact same length will have a chance to be missed if they are in two different split files. Thanks in advance for your help, Jean-Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Thu Mar 27 15:48:01 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Thu, 27 Mar 2014 15:48:01 +0100 Subject: [Inparanoid] InParanoid v4.1 does not work on more than 10000 sequences In-Reply-To: References: Message-ID: <53343A21.80407@scilifelab.se> Hi Jean-Nicolas, Sounds like your sequence files contains some weird characters that Blast chokes on. Use "od -c" to check, there should only be normal characters and \n in there. /Erik On 2014-03-27 13:59, Jean-Nicolas Audet, Mr wrote: > > Hello, > > I've been trying to make InParanoid work using de novo transcriptomes > of two non-model species (birds) I assembled with Trinity. They were > 'translated' to protein sequences using Transdecoder. The resulting > fasta file I'm trying to use in InParanoid looks like this (~30 000 seqs): > > >comp100291_c0_seq1 > > LPKKILLPIQQVLGHLLLALSYRGKVMQVKALKSKHEHNGPETLDAFLSSKLVVVKQPRE > > QAGFPLSIVFIPGEGRQERFLLHGEYNQSFCKEPVMELPRQ > > >comp102162_c0_seq1 > > PNMTLHFLKSSPGSWRLSGLVLIPYVTETISGSCETLTRLQMPAHIQQSRWKAKHGPRIL > > LLGLLQNLRSLFPLKVLPPGANSQLKRNCSFTSVCLIGTFYVESS > > >comp102206_c0_seq1 > > CQEQKWQKGNREEKGWAGVTVWGAYFPYLLIRCPNHQTSTPLSIHSQQHFMLCIIICPFS > > WLKPPVKTTQMFKGFFFKSGLKKFLALFLISWAAFATDRPLLGKQQSR > > I tried the example fasta files supplied with the program (called SC > and EC) and it works, but when I use my files, it's stuck at the first > step and it does not create any file (nor disk usage) after days. Here > is what I get with my fasta files: > > Loading module bio/ncbi-blast-2.2.22. > > Formatting BLAST databases > > Done formatting > > Starting BLAST searches... > > Starting first BLAST pass for bf - bf on [blastall] WARNING: the -C 3 > argument is currently experimental > > It then stays like this forever (I tried up to 6 days with 24 CPUs and > 256G). > > I also tried supplying my Blast results (inter-sample) generated > myself that I parsed with their supplied parser but then it still > stays forever at the same state, again without generating any file: > > Done BLAST searches. Starting ortholog detection... > > I tried with and without bootstraping, multitreading (-a16 option) or > not, as I said with or without supplied blast results and I also > cleaned my fasta files for any weird characters (removed annotations, > all ' * ', spaces, empty lines and dots. Now I'm running out of > ideas... I'm using a Unix cluster. I tried these jobs using up to 4 to > 24 CPUs with 8 to 256G memory. > > Finally, since it was working with SC and EC, I tried with a small > subset of my transcriptomes (a few thousands sequences) and it worked. > Thus it seems to me that the problem could be that InParanoid cannot > take more than, say, 10000 sequences. I could split my transcriptomes > into several smaller files of specified sequence ranges but then the > orthologs that do not have the exact same length will have a chance to > be missed if they are in two different split files. > > Thanks in advance for your help, > > Jean-Nicolas > > > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: