From aralp001 at udcf.gla.ac.uk Tue Jul 2 11:23:28 2002 From: aralp001 at udcf.gla.ac.uk (Dr Adam Ralph) Date: Tue, 2 Jul 2002 16:23:28 +0100 (BST) Subject: msf-pp Message-ID: Hi, I have been having trouble using W2H (version 4.0) with Emboss 2.4.1. When I specify MSF format output, I get an http error #500 "Premature end of script headers: msf-pp". Has anybody come across this problem before and is it fixable? Thanks Adam Dr. Adam Ralph Institute of Virology University of Glasgow Church Street Glasgow G11 5JR Phone: 0141 330 6268 Fax: 0141 337 2236 email: a.ralph at vir.gla.ac.uk From pemberaj at pugh.bip.bham.ac.uk Wed Jul 3 05:11:42 2002 From: pemberaj at pugh.bip.bham.ac.uk (Tony Pemberton) Date: Wed, 3 Jul 2002 10:11:42 +0100 Subject: Emboss and EMBL in GCG format In-Reply-To: Message-ID: Has anybody come across this problem: I am trying to index the latest release of EMBL 71.0 which has been converted to GCG format (for GCG). In both version 2.2.0 and 2.4.1, I get the following returned by dbigcg: Error accessing temp file. EMBOSS An error in dbigcg.c at line 565: Failed to open embl.acsrt2 for reading (2.2.0) Error accessing temp file. EMBOSS An error in embdbi.c at line 590: Cannot open embl.acnum_sort2 for reading (2.4.1) Is this an EMBL release size problem? Previous releases of EMBL have not shown this problem. I have the daily updates to EMBL as a separate database and they index normally. I therefore suspect it is a problem related to the ever increasing size of EMBL. Can anyone confirm? Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-6794 Medical School, E-mail: A.J.Pemberton at bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. ********************************************************************* From TimStrom at gsf.de Thu Jul 4 09:08:30 2002 From: TimStrom at gsf.de (Tim Strom) Date: Thu, 04 Jul 2002 15:08:30 +0200 Subject: jemboss wossname Message-ID: <3D2448CE.FF2AD3D5@gsf.de> I tried to run Jemboss in the standalone mode on sparc-solaris. I used emboss 2.4.1, jemboss-beta2.4 and java1.4. After starting jemboss, the progamm is not able to complete wossname. I am getting the following output: > java org.emboss.jemboss.Jemboss local Standalone mode /usr/local/packages/emboss-2.4.1/bin/wossname -colon -auto Now the process is busy but nothing happens. When I try to run wossname from the command line I am getting the following output: > /usr/local/packages/emboss-2.4.1/bin/wossname -colon -auto NUCLEIC:COMPOSITION compseq Counts the composition of dimer/trimer/etc words in a sequence NUCLEIC:PRIMERS primers Simple version of primer3 to pick PCR primers PROTEIN:2D STRUCTURE garnier Predicts protein secondary structure tmap Displays membrane spanning regions PROTEIN:COMPOSITION compseq Counts the composition of dimer/trimer/etc words in a sequence UTILS:DATABASE CREATION scope Convert raw scop classification file to embl-like format > Most of the installed emboss programms are not listed. Thus, it seems to be something wrong with wossname. Any hely? Tim -------------------------------------------------------------- Tim M. Strom Tel: +49 89 3187 3296 Institut fuer Humangenetik Fax: +49 89 3187 3297 Ingolstaedter Landstr. 1 85764 Neuherberg Germany WWW: http://ihg.gsf.de -------------------------------------------------------------- From simon.andrews at bbsrc.ac.uk Fri Jul 5 09:51:57 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Fri, 5 Jul 2002 14:51:57 +0100 Subject: Emboss and EMBL size problem Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E2860E@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Tony Pemberton [mailto:pemberaj at pugh.bip.bham.ac.uk] > Subject: Emboss and EMBL in GCG format > > Has anybody come across this problem: > > I am trying to index the latest release of EMBL 71.0 > In both version 2.2.0 and 2.4.1, I get the following > > Error accessing temp file. > > EMBOSS An error in dbigcg.c at line 565: > Failed to open embl.acsrt2 for reading > (2.2.0) > > [I] therefore suspect it is a problem related to the ever > increasing size of EMBL. Can anyone > confirm? I don't have a solution to this, but this is something which has bitten us this week so I thought I'd follow up with some observations from our group. We had problems trying to index the hum01.dat file from the latest EMBL release using dbiflat. We get a similar error to the above, with the program saying that it is unable to open the file. The file in this case comes in at about 2.4Gb. [As a side note, I thought that EMBL were supposed to ensure that none of the files in their releases got over 2Gb, so how did this one get through??] In our case we wrote a small Perl script to split the offending file into two smaller files, and the processing proceeded OK. The thing we haven't managed to establish is how we can get EMBOSS to cope with large files. We're running Linux with glibc2.2.4-24, which has support for large files (we can write short C scripts which will open and read 2Gb+ files), so why does EMBOSS not work with them? There are some notes on the web from an EMBOSS project meeting which suggest that EMBOSS should contain the appropriate code to work with >2Gb files, but they only talk about 64bit OSs, rather than 32bit systems with patched glibcs. http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Meetings/2000-08-02.html I also note that the configure script for EMBOSS identifies the command line options: --enable-large --enable-64 ..as well as many other text fragments which look like they might have something to do with this topic, but I've not been able to find any documentation about them, nor can I see anything in our configure log where the system is being checked for large file support. Since modern versions of 32-bit operating systems have glibc libraries which can cope with large files it would be extremely useful to have EMBOSS be able to use this functionality. Is anyone able to shed any light on the changes which would need to be made either to our configuration, or to the EMBOSS source code to allow large files to be accessed under systems such as ours. Many thanks Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From ableasby at hgmp.mrc.ac.uk Fri Jul 5 10:13:57 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 5 Jul 2002 15:13:57 +0100 (BST) Subject: Emboss and EMBL size problem Message-ID: <200207051413.PAA29668@bromine.hgmp.mrc.ac.uk> I suspect the above is a system problem which might be solved by (e.g.) limit descriptors 500 on the SGI Tony Pemberton mentioned. As far as large file support under linux is concerned you just need to add --enable-large to the configuration command. Alan From peter.rice at uk.lionbioscience.com Fri Jul 5 10:24:11 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 05 Jul 2002 15:24:11 +0100 Subject: Emboss and EMBL size problem References: <2DC41140A89ED411989D00508BDCD9ED01E2860E@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <3D25AC0B.3D4E2FCA@uk.lionbioscience.com> "simon andrews (BI)" wrote: > I also note that the configure script for EMBOSS identifies the command line options: > > --enable-large > --enable-64 > > ..as well as many other text fragments which look like they > might have something to do with this topic, but I've not been > able to find any documentation about them, nor can I see > anything in our configure log where the system is being checked > for large file support. They tell EMBOSS to use long integers and use large file support, but do not change the default integer size. > Is anyone able to shed any light on the changes which would need > to be made either to our configuration, or to the EMBOSS source > code to allow large files to be accessed under systems such as ours. I am investigating... One problem is that the specification for the index format EMBOSS uses does not support long integers. I will check with EBI (we use their EMBLCD format) on what they do. Splitting the file does sound like a good idea though. regards, Peter From ableasby at hgmp.mrc.ac.uk Fri Jul 5 11:02:30 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 5 Jul 2002 16:02:30 +0100 (BST) Subject: Emboss and EMBL size problem Message-ID: <200207051502.QAA05471@bromine.hgmp.mrc.ac.uk> An addendum, --enable-large allows EMBOSS to open large files but it will not allow correct indexing of >2Gb files at the moment. We'll look into that. You can sequentially scan through them though. Alan From gbottu at ben.vub.ac.be Fri Jul 5 12:46:09 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 5 Jul 2002 18:46:09 +0200 (CEST) Subject: EMBOSS under Staden ? Message-ID: <200207051646.SAA0001087526@ben.vub.ac.be> Dear colleagues, The Staden package can be used as X11 interface for EMBOSS. I have two questions : 1. Have some of you already treid it ? How good is it ? Are all the programs available ? 2. What about EMBnet nodes who want to offer Staden to their users ? Academics can get a free Staden licence, but what if a node has some industrial users ? Guy Bottu From qingjuan at wistar.upenn.edu Mon Jul 8 16:21:57 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Mon, 8 Jul 2002 16:21:57 -0400 Subject: No subject Message-ID: <200207081621.AA302973208@wistar.upenn.edu> Hi, I am configuring emboss for blast database. I copied part of database from balst formatted database into my test directory. Here is the files: # ls -l total 1308 -rwxr--r-- 1 root system 11306 Jul 8 13:52 alu.n.nhr -rwxr--r-- 1 root system 3988 Jul 8 13:52 alu.n.nin -rwxr--r-- 1 root system 16640 Jul 8 13:52 alu.n.nsd -rwxr--r-- 1 root system 411 Jul 8 13:52 alu.n.nsi -rwxr--r-- 1 root system 20336 Jul 8 13:52 alu.n.nsq -rwxr--r-- 1 nobody blast 41492 Feb 27 22:15 ecoli.nt.nhr -rwxr--r-- 1 nobody blast 4864 Feb 27 22:15 ecoli.nt.nin -rwxr--r-- 1 nobody blast 3200 Feb 27 22:15 ecoli.nt.nnd -rwxr--r-- 1 nobody blast 60 Feb 27 22:15 ecoli.nt.nni -rwxr--r-- 1 nobody blast 58320 Feb 27 22:15 ecoli.nt.nsd -rwxr--r-- 1 nobody blast 1264 Feb 27 22:15 ecoli.nt.nsi -rwxr--r-- 1 nobody blast 1165813 Feb 27 22:15 ecoli.nt.nsq When I run dbiblast command, there are some errors: # dbiblast Index a BLAST database Database name: ecoli Database directory [.]: Wildcard database filename [ecoli]: ecoli.* Release number [0.0]: Index date [00/00/00]: 07/08/02 N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 640: cannot open ./ecoli.nt.nhr table file ./ecoli.nt.nhr.nin Does anybody have some ideas? Thank you very much in advance. Grace From David.Bauer at SCHERING.DE Tue Jul 9 02:00:22 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 9 Jul 2002 08:00:22 +0200 Subject: Antwort: Message-ID: Hi Qingjuan, I know this problem. dbiblast expects to find the source fasta file which was used for formating the BLAST databases in the same directory. The 'Wildcard database filename' is used as base and then the .nin etc. are appended to this name. So the error says that dbiblast thinks 'ecoli.nt.nhr' is the fasta file and looks for a BLAST index file 'ecoli.nt.nhr.nin'. Either copy the fasta file in the same directory or create a symbolic link there. Then specify "ecoli.nt" as "Wildcard database filename" which in this case is not a wildcard. Peter, what about changing "Wildcard database filename" to "Filename of fasta source file" in dbiblast ? David. Hi, I am configuring emboss for blast database. I copied part of database from balst formatted database into my test directory. Here is the files: # ls -l total 1308 -rwxr--r-- 1 root system 11306 Jul 8 13:52 alu.n.nhr -rwxr--r-- 1 root system 3988 Jul 8 13:52 alu.n.nin -rwxr--r-- 1 root system 16640 Jul 8 13:52 alu.n.nsd -rwxr--r-- 1 root system 411 Jul 8 13:52 alu.n.nsi -rwxr--r-- 1 root system 20336 Jul 8 13:52 alu.n.nsq -rwxr--r-- 1 nobody blast 41492 Feb 27 22:15 ecoli.nt.nhr -rwxr--r-- 1 nobody blast 4864 Feb 27 22:15 ecoli.nt.nin -rwxr--r-- 1 nobody blast 3200 Feb 27 22:15 ecoli.nt.nnd -rwxr--r-- 1 nobody blast 60 Feb 27 22:15 ecoli.nt.nni -rwxr--r-- 1 nobody blast 58320 Feb 27 22:15 ecoli.nt.nsd -rwxr--r-- 1 nobody blast 1264 Feb 27 22:15 ecoli.nt.nsi -rwxr--r-- 1 nobody blast 1165813 Feb 27 22:15 ecoli.nt.nsq When I run dbiblast command, there are some errors: # dbiblast Index a BLAST database Database name: ecoli Database directory [.]: Wildcard database filename [ecoli]: ecoli.* Release number [0.0]: Index date [00/00/00]: 07/08/02 N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 640: cannot open ./ecoli.nt.nhr table file ./ecoli.nt.nhr.nin Does anybody have some ideas? Thank you very much in advance. Grace From ekolomiets at yahoo.com Tue Jul 9 12:47:23 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Tue, 9 Jul 2002 09:47:23 -0700 (PDT) Subject: EMBOSS Qs Message-ID: <20020709164723.27018.qmail@web13808.mail.yahoo.com> Hello, What can be wrong if my MSE from BMBASSY can not compile? I downloaded it and try to do make/make install/ and I am getting arrors like that: (attachment) Also there are processes running: re root 1077 0.0 0.9 81268 7668 ? S 12:22 0:00 /usr/sbin/httpd -DHAVE_ACCESS -DHAVE_PROXY -DHAVE_AUTH_ANON -DHAVE_AC apache 1119 0.0 1.0 81368 7884 ? S 12:22 0:00 /usr/sbin/httpd -DHAVE_ACCESS -DHAVE_PROXY -DHAVE_AUTH_ANON -DHAVE_AC Another question about database specifications. I created EMBOSS_DATA directory in /usr/local/EMBOSS-2.4.1/EMBOSS_DATA and in emboss.defaults uncommented embl, gb, and some other databases, but EMBOSS still use data only from test databases tembl, tgb and so on. Showdb - have all databases (test and newly added in a list). What other changes to emboss.defaults should i make? Thanks for your time! Elena Kolomiets Research Assistant Department of Plant Pathology Texas A&M University __________________________________________________ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: MSE-Errors Type: application/octet-stream Size: 2856 bytes Desc: MSE-Errors Url : http://lists.open-bio.org/pipermail/emboss/attachments/20020709/a0c9f62e/attachment.obj From qingjuan at wistar.upenn.edu Tue Jul 9 14:54:00 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 9 Jul 2002 14:54:00 -0400 Subject: dbiblast with newest blast database Message-ID: <200207091454.AA65470682@wistar.upenn.edu> Hi, I am configuring emboss with blast database. Because blast database upgrade new format since Feb., this year. the dbiblast can not support *.nal and *msk file extension. Does anybody have similar experience, and tell me how to make index with 'dbiblast' for blast database. Thank you very mcuh Grace From qingjuan at wistar.upenn.edu Tue Jul 9 17:34:28 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 9 Jul 2002 17:34:28 -0400 Subject: dbiblast command Message-ID: <200207091734.AA272367818@wistar.upenn.edu> Hi, When I use dbiblast command for chromosome database : # ls -l chromo* -rwx------ 1 root system 264482 Jul 9 17:28 chromosome.nhr -rwx------ 1 root system 24464 Jul 9 17:28 chromosome.nin -rwx------ 1 root system 16248 Jul 9 17:28 chromosome.nnd -rwx------ 1 root system 108 Jul 9 17:28 chromosome.nni -rwx------ 1 root system 178637 Jul 9 17:28 chromosome.nsd -rwx------ 1 root system 4092 Jul 9 17:28 chromosome.nsi -rwx------ 1 root system 134588104 Jul 9 17:28 chromosome.nsq -rwx------ 1 root system 84008 Jul 9 17:28 chromosome.ntd -rwx------ 1 root system 12368 Jul 9 17:28 chromosome.nti # dbiblast Index a BLAST database Database name: chromo Database directory [.]: Wildcard database filename [chromo]: chromosome.nin Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 547: failed to parse ' # Does anybody have ideas? what should I input for 'Wildcard databse filename' question? Thank you very much. Grace From cquijano at iib.uam.es Fri Jul 19 04:30:06 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Fri, 19 Jul 2002 10:30:06 +0200 Subject: eseqboot: Format problems Message-ID: <3D37CE0E.6020407@iib.uam.es> Hello, We are using eseqboot with all known formats, but by no way are we able to make it run fine. The information below is which w2h drops using FASTA format, and it appears to be an invalid format problem. First of all sorry if we are not using the correct input file type. But after reading de doc it seems clear that what eseqboot expects is an alignment input file. Does anybody know how to run it properly?* Thanks. Name*: /eseqboot/ *Started*: 02-07-19 10:01:56 *With Init file*: .. -datafile=lmb_2495.fasta -method=Seq -test=Boot -outfile=/home/cquijano/data/diskette/eseqboot_3574.outfile !embosstext --- end of init file : 02-07-19 10:01:56 *Exit*: 255 emboss: eseqboot -datafile=lmb_2495.fasta -method=Seq -test=Boot -outfile=/home/cquijano/data/diskette/eseqboot_3574.outfile -auto BAD OPTION CHARACTER: > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020719/f7e7e7ca/attachment.html From mbxlh at nottingham.ac.uk Tue Jul 23 04:50:31 2002 From: mbxlh at nottingham.ac.uk (Louise Honeyman) Date: Tue, 23 Jul 2002 09:50:31 +0100 Subject: Hi! Message-ID: Hi! I am wanting to use eprimer3 to design probes for in-situ hybridisation. I first need a pair of primers although the system will only allow mw to design a product of 200bp - I would ideally like something in the region of 400bp. Is there a way to change the settings to allow such? Also is there way to change the length of primers from 20bp? Thanks, Louise -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020723/7eec4318/attachment.html From sabino at area.ba.cnr.it Tue Jul 23 11:46:27 2002 From: sabino at area.ba.cnr.it (Liuni Sabino) Date: Tue, 23 Jul 2002 17:46:27 +0200 Subject: Help on emowse program Message-ID: <5.0.2.1.0.20020723174019.02397da0@194.119.200.100> Hi, I have building a database of protein sequences with dbifasta named orf. I have execute the program emowse (see below) % emowse Protein identification by mass spectrometry Input sequence(s): orf:* Input file: peptides.txt Whole sequence molwt [0]: Output file [pp000001.emowse]: Floating exception (core dumped) and the program exit for core dump. My input file is: 745.4311 752.4110 797.3966 839.1514 929.8979 982.4935 1091.6398 1116.7359 1199.7238 1232.6318 1260.6841 1278.8252 1307.6915 1320.7267 1345.6921 1513.7327 1627.9873 1683.8895 1716.2595 1829.0047 1887.8467 1951.9813 2023.3943 Any help for this problem. Thanks in advance Sabino Liuni ----------------------------------------------------- Bioinformatics and Genomic Group - C.N.R. Italian EMBnet Node Via Amendola 166/5 - 70126 Bari (Italy) Tel. +39-80-5482130 - Fax. +39-80-5482607 e_mail:sabino at area.ba.cnr.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020723/553714f4/attachment.html From ableasby at hgmp.mrc.ac.uk Tue Jul 23 12:01:07 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 23 Jul 2002 17:01:07 +0100 (BST) Subject: Help on emowse program Message-ID: <200207231601.RAA08191@bromine.hgmp.mrc.ac.uk> Sabino, Co-incidentally I am rewriting the successor to emowse at the moment (our Unit has recently purchased a mass spectrometer allowing the code to be tested first hand). I will look at your emowse problem. Alan From cbonnard at isrec-sg1.unil.ch Wed Jul 24 03:32:01 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 09:32:01 +0200 Subject: Interactive commands Message-ID: <10207240932.ZM4264@isrec-sg1> Hello, Any idea of the place to search for this problem? % dbiflat tsw EMBOSS An error in dbiflat.c at line 194: No files selected % I cannot find a way to get into any interactivity with (at least) this utility. Somehow frustrating.. Thanks for your advice, Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From David.Bauer at SCHERING.DE Wed Jul 24 03:44:59 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jul 2002 09:44:59 +0200 Subject: Antwort: Interactive commands Message-ID: Hi, just "dbiflat" without ANY paramter brings you in interactive mode. With "dbiflat -help" you get an overview of all options. And "tfm dbiflat" gives a more detailed explanation about the program. Hope this helps, David. Hello, Any idea of the place to search for this problem? % dbiflat tsw EMBOSS An error in dbiflat.c at line 194: No files selected % I cannot find a way to get into any interactivity with (at least) this utility. Somehow frustrating.. Thanks for your advice, Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From simon.andrews at bbsrc.ac.uk Wed Jul 24 03:49:36 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 24 Jul 2002 08:49:36 +0100 Subject: Interactive commands Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: cbonnard at isrec-sg1.unil.ch > Subject: Interactive commands > > > Hello, > > Any idea of the place to search for this problem? > > % dbiflat tsw > > EMBOSS An error in dbiflat.c at line 194: > No files selected > > I cannot find a way to get into any interactivity with (at > least) this utility. Hmmm. On my system: $ uname -sr Linux 2.4.9-21smp $ embossversion Writes the current EMBOSS version number 2.4.1 $ dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ Entry format [SWISS]: ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. Simon. From cbonnard at isrec-sg1.unil.ch Wed Jul 24 04:03:19 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 10:03:19 +0200 Subject: Interactive commands In-Reply-To: "simon andrews (BI)" "RE: Interactive commands" (Jul 24, 8:49am) References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <10207241003.ZM4334@isrec-sg1> Don't know what to say: the compilation went perfectly OK (as far as error messages...) $ uname -sr SunOS 5.8 % embossversion 2.4.1 %dbiflat Error: Too short (dbname) - minimum length is 1 characters %checktrans it hangs untill a CTRL-C 8-( >>>>> YES, obviously a config problem..but which ? I think that I will need some clue.. Thanks a lot! On Jul 24, 8:49am, simon andrews (BI) wrote: > Subject: RE: Interactive commands > > -----Original Message----- > > From: cbonnard at isrec-sg1.unil.ch > > Subject: Interactive commands > > > > > > Hello, > > > > Any idea of the place to search for this problem? > > > > % dbiflat tsw > > > > EMBOSS An error in dbiflat.c at line 194: > > No files selected > > > > I cannot find a way to get into any interactivity with (at > > least) this utility. > > Hmmm. On my system: > > $ uname -sr > Linux 2.4.9-21smp > > $ embossversion > Writes the current EMBOSS version number > 2.4.1 > > $ dbiflat > Index a flat file database > EMBL : EMBL > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > GB : Genbank, DDBJ > Entry format [SWISS]: > > ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. > > Simon. >-- End of excerpt from simon andrews (BI) -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From peter.rice at uk.lionbioscience.com Wed Jul 24 04:08:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Jul 2002 09:08:09 +0100 Subject: Interactive commands References: <10207240932.ZM4264@isrec-sg1> Message-ID: <3D3E6069.CE665EE4@uk.lionbioscience.com> Claude Bonnard wrote: > Any idea of the place to search for this problem? > % dbiflat tsw > EMBOSS An error in dbiflat.c at line 194: > No files selected > % > I cannot find a way to get into any interactivity with (at least) this utility. You can turn off the interactivity, but only for all applications (did you try any others?), if you try (csh): % setenv EMBOSS_FILTER Y or % setenv EMBOSS_AUTO Y (or if you have emboss_filter or emboss_auto defined in your emboss.defaults or ~/.embossrc files) These are just ways to put -filter or -auto on the command line for every application. You can hunt for them with -noauto or -nofilter on the command line to see whether these are causing your problem. The only parameter (no qualifier needed on the command line) for dbiflat is the database name. Everything else will be prompted for. OZE :-) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Wed Jul 24 04:20:14 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jul 2002 10:20:14 +0200 Subject: Interactive commands Message-ID: I'm running the 2.4.1 on SunOS 5.7 and it works perfectly. Probably this is a 5.8 specific issue. Hope someone with the same OS version can give you a hint. I have no idea... :--| Good luck! David Don't know what to say: the compilation went perfectly OK (as far as error messages...) $ uname -sr SunOS 5.8 % embossversion 2.4.1 %dbiflat Error: Too short (dbname) - minimum length is 1 characters %checktrans it hangs untill a CTRL-C 8-( >>>>> YES, obviously a config problem..but which ? I think that I will need some clue.. Thanks a lot! On Jul 24, 8:49am, simon andrews (BI) wrote: > Subject: RE: Interactive commands > > -----Original Message----- > > From: cbonnard at isrec-sg1.unil.ch > > Subject: Interactive commands > > > > > > Hello, > > > > Any idea of the place to search for this problem? > > > > % dbiflat tsw > > > > EMBOSS An error in dbiflat.c at line 194: > > No files selected > > > > I cannot find a way to get into any interactivity with (at > > least) this utility. > > Hmmm. On my system: > > $ uname -sr > Linux 2.4.9-21smp > > $ embossversion > Writes the current EMBOSS version number > 2.4.1 > > $ dbiflat > Index a flat file database > EMBL : EMBL > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > GB : Genbank, DDBJ > Entry format [SWISS]: > > ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. > > Simon. >-- End of excerpt from simon andrews (BI) -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From gwilliam at hgmp.mrc.ac.uk Wed Jul 24 04:25:54 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 24 Jul 2002 09:25:54 +0100 Subject: Interactive commands References: Message-ID: <3D3E6492.F2B76B92@hgmp.mrc.ac.uk> It works for me under 5.8: % uname -a SunOS californium 5.8 Generic_108528-11 sun4u sparc SUNW,Ultra-5_10 % dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ Entry format [SWISS]: Gary David.Bauer at SCHERING.DE wrote: > > I'm running the 2.4.1 on SunOS 5.7 and it works perfectly. > Probably this is a 5.8 specific issue. Hope someone with the same OS version can > give you a hint. > I have no idea... :--| > > Good luck! > David > > Don't know what to say: the compilation went perfectly OK (as far as error > messages...) > > $ uname -sr > SunOS 5.8 > % embossversion > 2.4.1 > %dbiflat > Error: Too short (dbname) - minimum length is 1 characters > %checktrans > > it hangs untill a CTRL-C 8-( > > >>>>> YES, obviously a config problem..but which ? > > I think that I will need some clue.. > > Thanks a lot! > > On Jul 24, 8:49am, simon andrews (BI) wrote: > > Subject: RE: Interactive commands > > > -----Original Message----- > > > From: cbonnard at isrec-sg1.unil.ch > > > Subject: Interactive commands > > > > > > > > > Hello, > > > > > > Any idea of the place to search for this problem? > > > > > > % dbiflat tsw > > > > > > EMBOSS An error in dbiflat.c at line 194: > > > No files selected > > > > > > I cannot find a way to get into any interactivity with (at > > > least) this utility. > > > > Hmmm. On my system: > > > > $ uname -sr > > Linux 2.4.9-21smp > > > > $ embossversion > > Writes the current EMBOSS version number > > 2.4.1 > > > > $ dbiflat > > Index a flat file database > > EMBL : EMBL > > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > > GB : Genbank, DDBJ > > Entry format [SWISS]: > > > > ..and it's all interactive from there on. Are you using an old Emboss > version? If not there might be a problem with your installation. > > > > Simon. > >-- End of excerpt from simon andrews (BI) > > -- > Claude Bonnard Ph.D. > ISREC (Swiss Institute for Experimental Cancer Research) > Bioinformatics Group > Ch des Boveresses 155 > CH-1066 Epalinges > Switzerland > phone: [41-21]-692-5891/-2236 > fax: [41-21]-652-6933 -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Wed Jul 24 04:34:53 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Jul 2002 09:34:53 +0100 Subject: Interactive commands References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> <10207241003.ZM4334@isrec-sg1> Message-ID: <3D3E66AD.56D20FC3@uk.lionbioscience.com> Claude Bonnard wrote: > > %checktrans > > it hangs untill a CTRL-C 8-( > > >>>>> YES, obviously a config problem..but which ? > > I think that I will need some clue.. That's a big clue. % checktrans -auto Error: Unable to read sequence '' % checktrans -filter ... hangs until you hit control-C ... or control-D ... because it is now defaulting to read standard input. Control-C will stop it, Control-D will say "Error: Unable to read sequence 'stdin'" Try: % checktrans -nofilter If that works, then look for an EMBOSS_FILTER definition somewhere. HTH Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From cbonnard at isrec-sg1.unil.ch Wed Jul 24 05:22:26 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 11:22:26 +0200 Subject: Interactive commands In-Reply-To: Peter Rice "Re: Interactive commands" (Jul 24, 9:34am) References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> <10207241003.ZM4334@isrec-sg1> <3D3E66AD.56D20FC3@uk.lionbioscience.com> Message-ID: <10207241122.ZM4512@isrec-sg1> Thanks a lot, Peter! This was -for an unknown reason the emboss.default which contained: set emboss_filter 1 removing it solved this . Thanks also to all of you for your very fast replies! Regards, Claude On Jul 24, 9:34am, Peter Rice wrote: > Subject: Re: Interactive commands > Claude Bonnard wrote: > > > > %checktrans > > > > it hangs untill a CTRL-C 8-( > > > > >>>>> YES, obviously a config problem..but which ? > > > > I think that I will need some clue.. > > That's a big clue. > > % checktrans -auto > Error: Unable to read sequence '' > > % checktrans -filter > ... hangs until you hit control-C ... or control-D ... because it is now > defaulting to read standard input. > > Control-C will stop it, Control-D will say "Error: Unable to read sequence > 'stdin'" > > Try: > > % checktrans -nofilter > > If that works, then look for an EMBOSS_FILTER definition somewhere. > > HTH > > Peter > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 >-- End of excerpt from Peter Rice -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From c_sanjib1 at rediffmail.com Thu Jul 25 08:40:36 2002 From: c_sanjib1 at rediffmail.com (Sanjib Chatterjee) Date: 25 Jul 2002 12:40:36 -0000 Subject: No subject Message-ID: <20020725124036.25980.qmail@mailFA11.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.open-bio.org/pipermail/emboss/attachments/20020725/a4632860/attachment.pl From peter.rice at uk.lionbioscience.com Thu Jul 25 11:45:14 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 25 Jul 2002 16:45:14 +0100 Subject: References: <20020725124036.25980.qmail@mailFA11.rediffmail.com> Message-ID: <3D401D0A.9A069042@uk.lionbioscience.com> Sanjib Chatterjee wrote: > > sir, > I want to know whether I can run the programme > "cpgreport" for a sequence of length 50 MB. Yes! EMBOSS will read any sequence length, it is limited by the memory on the machine. By default, EMBOSS reads the input sequence into a buffer while gussing the format. If you specify the format in the USA or on the command line it will use less memory for a very large sequence. For example: % cpgreport fasta::big.seq % cpgreport big.seq -sf fasta regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From qingjuan at wistar.upenn.edu Thu Jul 25 12:17:08 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Thu, 25 Jul 2002 12:17:08 -0400 Subject: dbiblast Message-ID: <200207251217.AA95682752@wistar.upenn.edu> >The answer is that you should use 'chromosome' as the wildcard >database name. Secondly, the author of dbiblast thinks there >might be some problems with the 2.4.1 version and this will >be corrected in 2.5.0 which is out soon. Thirdly, do not use >the very latest formatdb (NCBI have not yet released the >details of their index format so EMBOSS cannot index them). I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. I follow you instruction, it failed also. Here is the interactive result: # ls -l total 434903 -rwxr--r-- 1 nobody blast 76626843 Jul 4 22:09 patnt.nhr -rwxr--r-- 1 nobody blast 8066892 Jul 4 22:19 patnt.nin -rwxr--r-- 1 nobody blast 5377840 Jul 4 22:10 patnt.nnd -rwxr--r-- 1 nobody blast 21052 Jul 4 22:10 patnt.nni -rwxr--r-- 1 nobody blast 142820076 Jul 4 22:13 patnt.nsd -rwxr--r-- 1 nobody blast 2926655 Jul 4 22:19 patnt.nsi -rwxr--r-- 1 nobody blast 92506630 Jul 4 22:19 patnt.nsq -rwxr--r-- 1 nobody blast 119501 Jul 4 22:19 patnt.ntd -rwxr--r-- 1 nobody blast 17904 Jul 4 22:19 patnt.nti -rwxr--r-- 1 nobody blast 116819853 Jun 28 09:30 patnt.tar.gz # # dbiblast Index a BLAST database Database name: patnt Database directory [.]: Wildcard database filename [patnt]: patnt Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 333: No files selected # if i use patnt.nin in 'wildcard databse filename', that works without complain. but when I use seqret or other command to search the sequence, there are always error message: # ls -l total 435242 -rwxr-xr-x 1 root system 416 Jul 25 10:58 acnum.hit -rwxr-xr-x 1 root system 742 Jul 25 10:58 acnum.trg -rwxr-xr-x 1 root system 322 Jul 25 10:56 division.lkp -rwxr-xr-x 1 root system 338334 Jul 25 10:58 entrynam.idx -rwxr--r-- 1 nobody blast 76626843 Jul 4 22:09 patnt.nhr -rwxr--r-- 1 nobody blast 8066892 Jul 4 22:19 patnt.nin -rwxr--r-- 1 nobody blast 5377840 Jul 4 22:10 patnt.nnd -rwxr--r-- 1 nobody blast 21052 Jul 4 22:10 patnt.nni -rwxr--r-- 1 nobody blast 142820076 Jul 4 22:13 patnt.nsd -rwxr--r-- 1 nobody blast 2926655 Jul 4 22:19 patnt.nsi -rwxr--r-- 1 nobody blast 92506630 Jul 4 22:19 patnt.nsq -rwxr--r-- 1 nobody blast 119501 Jul 4 22:19 patnt.ntd -rwxr--r-- 1 nobody blast 17904 Jul 4 22:19 patnt.nti -rwxr--r-- 1 nobody blast 116819853 Jun 28 09:30 patnt.tar.gz # seqret Reads and writes (returns) sequences Input sequence(s): patnt:E00007.1 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:E00007.1' Input sequence(s): patnt:E00007 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:E00007' # seqret Reads and writes (returns) sequences Input sequence(s): patnt:2168318 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:2168318' Input sequence(s): patnt:2168314 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:2168314' # In my emboss.default: DB patnt [ type: N method: blast format: ncbi dir: /db4/users/qgu/test/test_dbi file: patnt.* indexdir: /db4/users/qgu/test/test_dbi release: "1.0" comment: "patnt formatted database --BLAST NCBI" ] Also, my fasta and genbank files works fine, only blast database can not work well. Your help will be highly appreciated. Grace From peter.rice at uk.lionbioscience.com Thu Jul 25 12:39:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 25 Jul 2002 17:39:09 +0100 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> Message-ID: <3D4029AD.23285B37@uk.lionbioscience.com> Qingjuan Gu (Grace) wrote: > > >Thirdly, do not use > >the very latest formatdb (NCBI have not yet released the > >details of their index format so EMBOSS cannot index them). > > I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. NCBI have changed the format of blast databases to "ASN.1 headers" (also known as 'format version 4') If you FTP the databases from NCBI you will probably get them in this format. We have asked NCBI for a description of the format. They promised to send one. Until then, the new blast format is not supported. I checked the latest code for the FASTA package, which has the same problem. Has anyone figured out how to decode this new blast database format yet? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Thu Jul 25 12:43:35 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Thu, 25 Jul 2002 18:43:35 +0200 Subject: dbiblast In-Reply-To: <200207251217.AA95682752@wistar.upenn.edu> References: <200207251217.AA95682752@wistar.upenn.edu> Message-ID: <20020725164335.GA3727@moulinette.dyndns.org> > # dbiblast > Index a BLAST database > Database name: patnt > Database directory [.]: > Wildcard database filename [patnt]: patnt I think the problem is that you are trying to format an already formatted database. You should get the flat file and format it instead. Charles From asen.nenov at metalife.de Thu Jul 25 15:35:36 2002 From: asen.nenov at metalife.de (Asen Nenov) Date: Thu, 25 Jul 2002 21:35:36 +0200 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> <3D4029AD.23285B37@uk.lionbioscience.com> Message-ID: <3D405308.5030709@metalife.de> I wish to suggest a way of understanding the BLAST asn format.. Of course this is last hope method. :-) Use the converters asn->xml of NCBI and do something with the output. Then reversibly reconstruct the data format. Enjoy. Regards Asen Nenov Peter Rice wrote: > Qingjuan Gu (Grace) wrote: > >>>Thirdly, do not use >>>the very latest formatdb (NCBI have not yet released the >>>details of their index format so EMBOSS cannot index them). >>> >>I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. >> > > NCBI have changed the format of blast databases to "ASN.1 headers" (also > known as 'format version 4') > > If you FTP the databases from NCBI you will probably get them in this > format. > > We have asked NCBI for a description of the format. They promised to send > one. > Until then, the new blast format is not supported. > > I checked the latest code for the FASTA package, which has the same > problem. > > Has anyone figured out how to decode this new blast database format yet? > > regards, > > Peter Rice > > -- Best Regards Asen Nenov METALIFE AG asen.nenov at metalife.de www.metalife.de From peter.rice at uk.lionbioscience.com Fri Jul 26 06:48:50 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 26 Jul 2002 11:48:50 +0100 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> <3D4029AD.23285B37@uk.lionbioscience.com> <3D405308.5030709@metalife.de> Message-ID: <3D412912.4A934BF1@uk.lionbioscience.com> Asen Nenov wrote: > > I wish to suggest a way of understanding the BLAST asn format.. Of > course this is last hope method. :-) > Use the converters asn->xml of NCBI and do something with the output. > Then reversibly reconstruct the data format. Enjoy. Unfortunately ... the blast databases have a *binary* format. No way to convert this into ASN.1 (which EMBOSS could probably parse more easily than XML). I suppose reading the formatdb source code might help .... but it would really help if NCBI could document their format. I'm sure they know other software (EMBOSS, fasta, and others) is reading blast database files. regards, Peter From sebastian.bassi at ar.advantaseeds.com Mon Jul 29 04:29:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Mon, 29 Jul 2002 10:29:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A954514D59@e2knl1.nl.seedsnetwork.com> Hi, I?ve found 2 problems with EMBOSS. I?ve installed this in the past under Solaris 7 (Sun) and several flavors of Linux. Now I?m trying to compile it under Red Hat 6.2 server. The configure stage goes by OK, but when I try to compile I get: gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_ STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.4.1\" -D STDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE _STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDI NT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H= 1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_U NISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FOR K=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DX_DISPLAY_MISSING=1 -DHAVE_LIBM=1 -I. - I. -I../nucleus -I../ajax -I../plplot -I/usr/local -DNO_AUTH -g -O2 -c `test - f 'abiview.c' || echo './'`abiview.c /bin/sh ../libtool --mode=link gcc -g -O2 -o abiview abiview.o ../nucleus/li bnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -lX11 -lm mkdir .libs gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.l ibs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -lX11 -lm -Wl,--rpath -Wl,/usr/local/lib /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[2]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make: *** [all-recursive] Error 1 [root at pescadilla EMBOSS-2.4.1]# Perhaps it?s something related to graphics, since is a server machine, X is not installed. Is X needed in order to compile it? I really need to use only text based programs from EMBOSS. If there?s a program witch needs X, I would like not to compile it but keep on working with the command line (CL) ones. Now, it seems that I can?t compile even CL programs because I don?t have X installed. Maybe I?m wrong. I also reporting that EMNU program is not where the EMBASSY web page states it is: ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.4.tar.gz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020729/18925b5d/attachment.html From jcurole at cisunix.unh.edu Mon Jul 29 11:07:02 2002 From: jcurole at cisunix.unh.edu (Jason Curole) Date: Mon, 29 Jul 2002 11:07:02 -0400 Subject: Compiling EMBOSS 2.4.1 on Mac OS X Message-ID: Dear users, I am trying to compile the EMBOSS 2.4.1 package on OS X. I have installed X Darwin and this runs okay. I run configure and that also seem to run okay. I then make and it runs for a while but eventually bombs out on the error make[3]: *** No rule to make target `alignment_differences_group.html',. The last few lines of terminal text prior to the fail are pasted in below. I appreciate any help anyone could provide. Thanks, Jason Making install in wormpep make[3]: Nothing to be done for `install-exec-am'. /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/test/wormpep mkdir /usr/local/share/EMBOSS/test/wormpep /usr/bin/install -c -m 644 wormpep /usr/local/share/EMBOSS/test/wormpep/wormpep /usr/bin/install -c -m 644 acnum.hit /usr/local/share/EMBOSS/test/wormpep/acnum.hit /usr/bin/install -c -m 644 acnum.trg /usr/local/share/EMBOSS/test/wormpep/acnum.trg /usr/bin/install -c -m 644 division.lkp /usr/local/share/EMBOSS/test/wormpep/division.lkp /usr/bin/install -c -m 644 entrynam.idx /usr/local/share/EMBOSS/test/wormpep/entrynam.idx /usr/bin/install -c -m 644 des.hit /usr/local/share/EMBOSS/test/wormpep/des.hit /usr/bin/install -c -m 644 des.trg /usr/local/share/EMBOSS/test/wormpep/des.trg make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. Making install in doc Making install in manuals make[3]: Nothing to be done for `install-exec-am'. /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/doc/manuals mkdir /usr/local/share/EMBOSS/doc mkdir /usr/local/share/EMBOSS/doc/manuals /usr/bin/install -c -m 644 admin.sty /usr/local/share/EMBOSS/doc/manuals/admin.sty /usr/bin/install -c -m 644 admin.tex /usr/local/share/EMBOSS/doc/manuals/admin.tex /usr/bin/install -c -m 644 admin.aux /usr/local/share/EMBOSS/doc/manuals/admin.aux /usr/bin/install -c -m 644 admin.dvi /usr/local/share/EMBOSS/doc/manuals/admin.dvi /usr/bin/install -c -m 644 admin.log /usr/local/share/EMBOSS/doc/manuals/admin.log /usr/bin/install -c -m 644 admin.pdf /usr/local/share/EMBOSS/doc/manuals/admin.pdf /usr/bin/install -c -m 644 admin.ps /usr/local/share/EMBOSS/doc/manuals/admin.ps /usr/bin/install -c -m 644 admin.toc /usr/local/share/EMBOSS/doc/manuals/admin.toc /usr/bin/install -c -m 644 adminguide.tar.gz /usr/local/share/EMBOSS/doc/manuals/adminguide.tar.gz /usr/bin/install -c -m 644 program.ps.gz /usr/local/share/EMBOSS/doc/manuals/program.ps.gz /usr/bin/install -c -m 644 EMBOSS-FreeBSD-HOWTO.txt /usr/local/share/EMBOSS/doc/manuals/EMBOSS-FreeBSD-HOWTO.txt /usr/bin/install -c -m 644 emboss_qg.pdf /usr/local/share/EMBOSS/doc/manuals/emboss_qg.pdf /usr/bin/install -c -m 644 emboss_qg.ps /usr/local/share/EMBOSS/doc/manuals/emboss_qg.ps Making install in programs Making install in html make[3]: *** No rule to make target `alignment_differences_group.html', needed by `all-am'. Stop. make[2]: *** [install-recursive] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [install-recursive] Error 1 Jason P. Curole Hubbard Center for Genome Studies and Program in Genetics Genomics I ETB 35 Colovos Road University of New Hampshire Durham NH 03824-3534 http://tilapia.unh.edu/WWWPages/curole/curole.html From sebastian.bassi at ar.advantaseeds.com Mon Jul 29 09:38:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Mon, 29 Jul 2002 15:38:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A9544F6E4E@e2knl1.nl.seedsnetwork.com> ______________________________ Forward Header __________________________________ Subject: Re[2]: Instalation and D'd problem. Author: Sebastian Bassi at MOBILE-KAPELLE Date: 7/29/2002 3:31 PM Hello, After trying the "wihout x" option, I?ve got the same error. I did: # ./configure --without-x --x-includes="" --x-libraries="" (before that I did a "make clean" in order to start againg). Then, after the make command I got: [a lot output deleted] gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.l ibs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -lX11 -lm -Wl,--rpath -Wl,/usr/local/lib /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[2]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make: *** [all-recursive] Error 1 [root at pescadilla EMBOSS-2.4.1]# ______________________________ Reply Separator _________________________________ Subject: Re: Instalation and D'd problem. Author: "ableasby at hgmp.mrc.ac.uk" at exkapelle Date: 7/29/2002 4:08 PM Thanks for the EMNU information. As far as X11 goes it is a known problem and is on the list of things to do. Please try configuring with: --without-x --x-includes="" --x-libraries="" and let me know if that solves it for you. Rgds Alan Bleasby HGMP -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020729/6c298c7a/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Forward.txt Url: http://lists.open-bio.org/pipermail/emboss/attachments/20020729/6c298c7a/attachment.txt From rgrams at alpha.tu.ac.th Tue Jul 30 02:52:20 2002 From: rgrams at alpha.tu.ac.th (Rudi Grams) Date: Tue, 30 Jul 2002 13:52:20 +0700 Subject: Compiling EMBOSS 2.4.1 on Mac OS X Message-ID: <3D44B0C4@email.tu.ac.th> Any chance that you used stuffit expander to extract the emboss archive? Stuffit cannot deal with long file names and will change the names of such files! alignment_differences_group.html and others of the html files exceed the name length that stuffit can handle. Better use the unix tools as described in the manual. By the way I'am working on a simple GUI for emboss apps done in AppleScript Studio, similar to the Linux/Kaptain interface by Thomas Siegmund. If there is any interest please let me know... Kindly, Rudi Rudi Grams Faculty of Allied Health Sciences Thammasat University Rangsit Campus Pathum Thani 12121 Thailand From abrown at nimr.mrc.ac.uk Tue Jul 30 09:36:27 2002 From: abrown at nimr.mrc.ac.uk (Alex Brown) Date: Tue, 30 Jul 2002 14:36:27 +0100 Subject: Some help required. Message-ID: <5911EB42-A3C1-11D6-B96B-0003938768AC@nimr.mrc.ac.uk> Hi. Firstly, let me apologize for what may seem a trivial problem, but I have nowhere else to turn. I have 'used' UNIX previously, but only as a user (and not very often at that), and not as an administrator, and the problem is getting EMBOSS to function properly. I have installed EMBOSS on a Macintosh PowerBook G4, under Darwin. I am also running XDarwin (XFree86 4.2.0). After installation and running 'make install', 'wossname -auto | less' gives a long list of programs, as stated in the EMBOSS Administrators Guide, section 2.3.5. All the program files are located in the /usr/local/bin directory - I notice that there is no EMBOSS entries in /usr/share/man. Is this correct ? In order to get the 'showdb' command to list the available databases, I uncommented the first line of the emboss.default.template file (SET emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to emboss.default. The command 'showdb' results in the following output: # Name Type ID Qry All Comment # ==== ==== == === === ======= tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD-ROM index tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index indicating the databases in the /local/share/EMBOSS/test directory. So far so good. However, attempting to work through the tutorial on the EMBOSS web-site, I find that I am unable to access the databases: for example [xxxxxx:~] me% seqret Reads and writes (returns) sequences Input sequence(s): tembl:hs* Warning: Cannot open division file '' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hs*' Input sequence(s): I was assuming that the databases that came with the installation would work, and would allow me to work round to installing my own databases. The above would indicate that there is still something I have yet to do. Could someone please offer me some guidance on this. Many thanks. Alex Brown. From qingjuan at wistar.upenn.edu Tue Jul 30 10:27:36 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 30 Jul 2002 10:27:36 -0400 Subject: Some help required. Message-ID: <200207301027.AA112197860@wistar.upenn.edu> The possible reason for this: your 'real database' have permission problem, double-check your 'tembl' database mod. ---------- Original Message ---------------------------------- From: Alex Brown Date: Tue, 30 Jul 2002 14:36:27 +0100 >Hi. > >Firstly, let me apologize for what may seem a trivial problem, but I >have nowhere else to turn. I have 'used' UNIX previously, but only as a >user (and not very often at that), and not as an administrator, and the >problem is getting EMBOSS to function properly. > >I have installed EMBOSS on a Macintosh PowerBook G4, under Darwin. I am >also running XDarwin (XFree86 4.2.0). After installation and running >'make install', 'wossname -auto | less' gives a long list of programs, >as stated in the EMBOSS Administrators Guide, section 2.3.5. > >All the program files are located in the /usr/local/bin directory - I >notice that there is no EMBOSS entries in /usr/share/man. Is this >correct ? > >In order to get the 'showdb' command to list the available databases, I >uncommented the first line of the emboss.default.template file (SET >emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to >emboss.default. The command 'showdb' results in the following output: > ># Name Type ID Qry All Comment ># ==== ==== == === === ======= >tpir P OK OK OK PIR using NBRF access for 4 files >tsw P OK OK OK Swissprot native format with EMBL CD-ROM >index >tswnew P OK OK OK Swissnew as 3 files in native format with >EMBL CD-ROM index >twp P OK OK OK EMBL new in native format with EMBL >CD-ROM index >tembl N OK OK OK EMBL in native format with EMBL CD-ROM >index >tgb N OK - - Genbank IDs >tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM >index > >indicating the databases in the /local/share/EMBOSS/test directory. > >So far so good. > >However, attempting to work through the tutorial on the EMBOSS web-site, >I find that I am unable to access the databases: for example > >[xxxxxx:~] me% seqret >Reads and writes (returns) sequences >Input sequence(s): tembl:hs* >Warning: Cannot open division file '' >Warning: seqCdQry failed >Error: Unable to read sequence 'tembl:hs*' >Input sequence(s): > >I was assuming that the databases that came with the installation would >work, and would allow me to work round to installing my own databases. >The above would indicate that there is still something I have yet to do. >Could someone please offer me some guidance on this. > >Many thanks. > >Alex Brown. > > From peter.rice at uk.lionbioscience.com Tue Jul 30 11:00:06 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 30 Jul 2002 16:00:06 +0100 Subject: Some help required. References: <5911EB42-A3C1-11D6-B96B-0003938768AC@nimr.mrc.ac.uk> Message-ID: <3D46A9F6.C6296B06@uk.lionbioscience.com> Alex Brown wrote: > In order to get the 'showdb' command to list the available databases, I > uncommented the first line of the emboss.default.template file (SET > emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to > emboss.default. The command 'showdb' results in the following output: > > indicating the databases in the /local/share/EMBOSS/test directory. > > So far so good. > > However, attempting to work through the tutorial on the EMBOSS web-site, > I find that I am unable to access the databases: for example > > [xxxxxx:~] me% seqret > Reads and writes (returns) sequences > Input sequence(s): tembl:hs* > Warning: Cannot open division file '' > Warning: seqCdQry failed > Error: Unable to read sequence 'tembl:hs*' > Input sequence(s): First, I assume your emboss.default file has: SET emboss_tempdata /local/share/EMBOSS/test Next, you can try: seqret -debug This will write a file seqret.dbg where I would expect lines like this: directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*' ajFileNewIn '/local/share/EMBOSS/test/embl/division.lkp' ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp' This is the division file which it says cannot be opened. If you see what appears to be the right filename, check file (and directory) protection. If you see something else, it may give a clue to where the setup is wrong, or you can get help from emboss-bug at embnet.org regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From naofumi at mac.com Tue Jul 30 11:34:50 2002 From: naofumi at mac.com (Naofumi Kagami) Date: Wed, 31 Jul 2002 00:34:50 +0900 Subject: Compiling EMBOSS 2.4.1 on Mac OS X In-Reply-To: Message-ID: Hi Jason, I just solved that one today. I think that the problem lies with Stuffit Expander. If you look into EMBOSS-2.4.1/doc/programs/html after expanding the archive, you will notice that the file 'alignment_differences_group.html' is missing the final 'l' in '.html'. The makefile is looking for '`alignment_differences_group.html' but only finds '`alignment_differences_group.htm', so it sends out an error and quits. At least that's what I'm guessing. I'm no UNIX expert myself :-). I am guessing that Stuffit Expander is choking on long filenames (the legacy of Classic) since the truncation is occurring after the 30th letter. After adding the final 'l' to the filename, do a make once more. You'll find other errors that have to be solved in the same way. After doing this several times, make should finish without errors. Then you can make install. Hope this works for you. Naofumi Kagami On 2002.07.30, at 00:07, Jason Curole wrote: > . I run configure and that also seem to run okay. > I then make and it runs for a while but eventually bombs out on the > error > make[3]: *** No rule to make target `alignment_differences_group.html',. > The last few lines of terminal text prior to the fail are pasted in > below. > I appreciate any help anyone could provide. > > Thanks, Jason > > Making install in wormpep > make[3]: Nothing to be done for `install-exec-am'. > /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/test/wormpep > mkdir /usr/local/share/EMBOS From abrown at nimr.mrc.ac.uk Tue Jul 30 11:56:13 2002 From: abrown at nimr.mrc.ac.uk (Alex Brown) Date: Tue, 30 Jul 2002 16:56:13 +0100 Subject: Some help required. In-Reply-To: <3D46A9F6.C6296B06@uk.lionbioscience.com> Message-ID: OUCH !! (just me kicking myself). Initially, the emboss.default file had the line: SET emboss_tempdata path_to_directory_$EMBOSS/test I had assumed thet 'path_to_directory_$EMBOSS was a variable holding the path. Apparently not so. I edited this line as you suggested: SET emboss_tempdata /local/share/EMBOSS/test but again this didn't solve the problem. However, changing it to: SET emboss_tempdata /usr/local/share/EMBOSS/test did work. That might have been the root of the problem (groan !!) Many thanks for all the replies. Alex Brown. On Tuesday, July 30, 2002, at 04:00 PM, Peter Rice wrote: > First, I assume your emboss.default file has: > > SET emboss_tempdata /local/share/EMBOSS/test > > Next, you can try: > > seqret -debug > > This will write a file seqret.dbg where I would expect lines like this: > > directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*' > ajFileNewIn '/local/share/EMBOSS/test/embl/division.lkp' > ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp' > > This is the division file which it says cannot be opened. > > If you see what appears to be the right filename, check file (and > directory) protection. > > If you see something else, it may give a clue to where the setup is > wrong, > or you can get help from emboss-bug at embnet.org > > regards, > > Peter Rice > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 > From sebastian.bassi at ar.advantaseeds.com Wed Jul 31 03:36:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Wed, 31 Jul 2002 09:36:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A9544F9397@e2knl1.nl.seedsnetwork.com> Hi, I installed the rpm you point me and it works!!!! Here is a proposed question (and answer) for the EMBOSS FAQ (under INSTALLATION). Q) Is there a way to install EMBOSS without X? (like in a text only server machine) A) Yes, you only need to install XFree86-devel package before configuring and compiling EMBOSS. (tried on a Red Hat 6.2 server installation). Thank you for your help.- PS: I?ll make a copy of this mail to the mailing list since it could help somebody else. ______________________________ Reply Separator _________________________________ Subject: RE: Instalation and D'd problem. Author: "ableasby at hgmp.mrc.ac.uk" at exkapelle Date: 7/31/2002 1:39 AM btw: I have been assuming all along that you categorically don't want X11 on your server. If that is not the case then, as I see you're using RedHat, all you need to install for emboss to compile is the XFree86-devel rpm. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020731/12123691/attachment.html From shibl at seqbio.com Wed Jul 31 11:55:52 2002 From: shibl at seqbio.com (Shibl Mourad) Date: Wed, 31 Jul 2002 11:55:52 -0400 Subject: Supermatcher References: <2AE73E3601DA0E428E14535564F6A9544F9397@e2knl1.nl.seedsnetwork.com> Message-ID: <01b101c238aa$c082d270$2602a8c0@SEQUENCE> RE: Instalation and D'd problem.Hi all, I am using supermatcher to align 2 sequences, and it seems that the order of the sequences affects the results dramatically (see example below). Is that normal? Shibl Note: The following examples where build by downloading AP000926.5 and AP001970.3 from entrez and then calling supermatcher with wordlen=20, all other parameters are kept as default. ######################################## # Program: supermatcher # Rundate: Wed Jul 31 11:54:34 2002 # Report_file: ap000926.supermatcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: AP000926.5 # 2: AP001970.3 # Matrix: EDNAFULL # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 57265 # Identity: 40361/57265 (70.5%) # Similarity: 40361/57265 (70.5%) # Gaps: 11627/57265 (20.3%) # Score: 133850.5 # # #======================================= ######################################## # Program: supermatcher # Rundate: Wed Jul 31 11:55:10 2002 # Report_file: ap001970.supermatcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: AP001970.3 # 2: AP000926.5 # Matrix: EDNAFULL # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 52182 # Identity: 50101/52182 (96.0%) # Similarity: 50101/52182 (96.0%) # Gaps: 1463/52182 ( 2.8%) # Score: 242805.0 # # #======================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020731/120d8f72/attachment.html From qingjuan at wistar.upenn.edu Wed Jul 31 16:32:21 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Wed, 31 Jul 2002 16:32:21 -0400 Subject: PNG format output Message-ID: <200207311632.AA140050702@wistar.upenn.edu> Hi, When I use 'dottup' and choose 'PNG' output format, there is a error message: Error: Invalid graph value 'png' oth in command line and on web site. But when I check http://bioinfo.pbi.nrc.ca:8090/EMBOSS/, the png format can work in this site. Does anybody give me some suggestions about this problem. Thanks a lot. Grace athena.wistar.upenn.edu> dottup Displays a wordmatch dotplot of two sequences Input sequence: tembl:xlrhodop Second sequence: tembl:xlrhodop Word size [10]: Display as data [N]: Graph type [x11]: png Error: Invalid graph value 'png' Devices allowed are:- postscript From aralp001 at udcf.gla.ac.uk Tue Jul 2 15:23:28 2002 From: aralp001 at udcf.gla.ac.uk (Dr Adam Ralph) Date: Tue, 2 Jul 2002 16:23:28 +0100 (BST) Subject: msf-pp Message-ID: Hi, I have been having trouble using W2H (version 4.0) with Emboss 2.4.1. When I specify MSF format output, I get an http error #500 "Premature end of script headers: msf-pp". Has anybody come across this problem before and is it fixable? Thanks Adam Dr. Adam Ralph Institute of Virology University of Glasgow Church Street Glasgow G11 5JR Phone: 0141 330 6268 Fax: 0141 337 2236 email: a.ralph at vir.gla.ac.uk From pemberaj at pugh.bip.bham.ac.uk Wed Jul 3 09:11:42 2002 From: pemberaj at pugh.bip.bham.ac.uk (Tony Pemberton) Date: Wed, 3 Jul 2002 10:11:42 +0100 Subject: Emboss and EMBL in GCG format In-Reply-To: Message-ID: Has anybody come across this problem: I am trying to index the latest release of EMBL 71.0 which has been converted to GCG format (for GCG). In both version 2.2.0 and 2.4.1, I get the following returned by dbigcg: Error accessing temp file. EMBOSS An error in dbigcg.c at line 565: Failed to open embl.acsrt2 for reading (2.2.0) Error accessing temp file. EMBOSS An error in embdbi.c at line 590: Cannot open embl.acnum_sort2 for reading (2.4.1) Is this an EMBL release size problem? Previous releases of EMBL have not shown this problem. I have the daily updates to EMBL as a separate database and they index normally. I therefore suspect it is a problem related to the ever increasing size of EMBL. Can anyone confirm? Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-6794 Medical School, E-mail: A.J.Pemberton at bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. ********************************************************************* From TimStrom at gsf.de Thu Jul 4 13:08:30 2002 From: TimStrom at gsf.de (Tim Strom) Date: Thu, 04 Jul 2002 15:08:30 +0200 Subject: jemboss wossname Message-ID: <3D2448CE.FF2AD3D5@gsf.de> I tried to run Jemboss in the standalone mode on sparc-solaris. I used emboss 2.4.1, jemboss-beta2.4 and java1.4. After starting jemboss, the progamm is not able to complete wossname. I am getting the following output: > java org.emboss.jemboss.Jemboss local Standalone mode /usr/local/packages/emboss-2.4.1/bin/wossname -colon -auto Now the process is busy but nothing happens. When I try to run wossname from the command line I am getting the following output: > /usr/local/packages/emboss-2.4.1/bin/wossname -colon -auto NUCLEIC:COMPOSITION compseq Counts the composition of dimer/trimer/etc words in a sequence NUCLEIC:PRIMERS primers Simple version of primer3 to pick PCR primers PROTEIN:2D STRUCTURE garnier Predicts protein secondary structure tmap Displays membrane spanning regions PROTEIN:COMPOSITION compseq Counts the composition of dimer/trimer/etc words in a sequence UTILS:DATABASE CREATION scope Convert raw scop classification file to embl-like format > Most of the installed emboss programms are not listed. Thus, it seems to be something wrong with wossname. Any hely? Tim -------------------------------------------------------------- Tim M. Strom Tel: +49 89 3187 3296 Institut fuer Humangenetik Fax: +49 89 3187 3297 Ingolstaedter Landstr. 1 85764 Neuherberg Germany WWW: http://ihg.gsf.de -------------------------------------------------------------- From simon.andrews at bbsrc.ac.uk Fri Jul 5 13:51:57 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Fri, 5 Jul 2002 14:51:57 +0100 Subject: Emboss and EMBL size problem Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E2860E@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: Tony Pemberton [mailto:pemberaj at pugh.bip.bham.ac.uk] > Subject: Emboss and EMBL in GCG format > > Has anybody come across this problem: > > I am trying to index the latest release of EMBL 71.0 > In both version 2.2.0 and 2.4.1, I get the following > > Error accessing temp file. > > EMBOSS An error in dbigcg.c at line 565: > Failed to open embl.acsrt2 for reading > (2.2.0) > > [I] therefore suspect it is a problem related to the ever > increasing size of EMBL. Can anyone > confirm? I don't have a solution to this, but this is something which has bitten us this week so I thought I'd follow up with some observations from our group. We had problems trying to index the hum01.dat file from the latest EMBL release using dbiflat. We get a similar error to the above, with the program saying that it is unable to open the file. The file in this case comes in at about 2.4Gb. [As a side note, I thought that EMBL were supposed to ensure that none of the files in their releases got over 2Gb, so how did this one get through??] In our case we wrote a small Perl script to split the offending file into two smaller files, and the processing proceeded OK. The thing we haven't managed to establish is how we can get EMBOSS to cope with large files. We're running Linux with glibc2.2.4-24, which has support for large files (we can write short C scripts which will open and read 2Gb+ files), so why does EMBOSS not work with them? There are some notes on the web from an EMBOSS project meeting which suggest that EMBOSS should contain the appropriate code to work with >2Gb files, but they only talk about 64bit OSs, rather than 32bit systems with patched glibcs. http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Meetings/2000-08-02.html I also note that the configure script for EMBOSS identifies the command line options: --enable-large --enable-64 ..as well as many other text fragments which look like they might have something to do with this topic, but I've not been able to find any documentation about them, nor can I see anything in our configure log where the system is being checked for large file support. Since modern versions of 32-bit operating systems have glibc libraries which can cope with large files it would be extremely useful to have EMBOSS be able to use this functionality. Is anyone able to shed any light on the changes which would need to be made either to our configuration, or to the EMBOSS source code to allow large files to be accessed under systems such as ours. Many thanks Simon. -- Simon Andrews PhD Bioinformatics Dept The Babraham Institute simon.andrews at bbsrc.ac.uk +44 (0)1223 496463 From ableasby at hgmp.mrc.ac.uk Fri Jul 5 14:13:57 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 5 Jul 2002 15:13:57 +0100 (BST) Subject: Emboss and EMBL size problem Message-ID: <200207051413.PAA29668@bromine.hgmp.mrc.ac.uk> I suspect the above is a system problem which might be solved by (e.g.) limit descriptors 500 on the SGI Tony Pemberton mentioned. As far as large file support under linux is concerned you just need to add --enable-large to the configuration command. Alan From peter.rice at uk.lionbioscience.com Fri Jul 5 14:24:11 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 05 Jul 2002 15:24:11 +0100 Subject: Emboss and EMBL size problem References: <2DC41140A89ED411989D00508BDCD9ED01E2860E@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <3D25AC0B.3D4E2FCA@uk.lionbioscience.com> "simon andrews (BI)" wrote: > I also note that the configure script for EMBOSS identifies the command line options: > > --enable-large > --enable-64 > > ..as well as many other text fragments which look like they > might have something to do with this topic, but I've not been > able to find any documentation about them, nor can I see > anything in our configure log where the system is being checked > for large file support. They tell EMBOSS to use long integers and use large file support, but do not change the default integer size. > Is anyone able to shed any light on the changes which would need > to be made either to our configuration, or to the EMBOSS source > code to allow large files to be accessed under systems such as ours. I am investigating... One problem is that the specification for the index format EMBOSS uses does not support long integers. I will check with EBI (we use their EMBLCD format) on what they do. Splitting the file does sound like a good idea though. regards, Peter From ableasby at hgmp.mrc.ac.uk Fri Jul 5 15:02:30 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 5 Jul 2002 16:02:30 +0100 (BST) Subject: Emboss and EMBL size problem Message-ID: <200207051502.QAA05471@bromine.hgmp.mrc.ac.uk> An addendum, --enable-large allows EMBOSS to open large files but it will not allow correct indexing of >2Gb files at the moment. We'll look into that. You can sequentially scan through them though. Alan From gbottu at ben.vub.ac.be Fri Jul 5 16:46:09 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 5 Jul 2002 18:46:09 +0200 (CEST) Subject: EMBOSS under Staden ? Message-ID: <200207051646.SAA0001087526@ben.vub.ac.be> Dear colleagues, The Staden package can be used as X11 interface for EMBOSS. I have two questions : 1. Have some of you already treid it ? How good is it ? Are all the programs available ? 2. What about EMBnet nodes who want to offer Staden to their users ? Academics can get a free Staden licence, but what if a node has some industrial users ? Guy Bottu From qingjuan at wistar.upenn.edu Mon Jul 8 20:21:57 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Mon, 8 Jul 2002 16:21:57 -0400 Subject: No subject Message-ID: <200207081621.AA302973208@wistar.upenn.edu> Hi, I am configuring emboss for blast database. I copied part of database from balst formatted database into my test directory. Here is the files: # ls -l total 1308 -rwxr--r-- 1 root system 11306 Jul 8 13:52 alu.n.nhr -rwxr--r-- 1 root system 3988 Jul 8 13:52 alu.n.nin -rwxr--r-- 1 root system 16640 Jul 8 13:52 alu.n.nsd -rwxr--r-- 1 root system 411 Jul 8 13:52 alu.n.nsi -rwxr--r-- 1 root system 20336 Jul 8 13:52 alu.n.nsq -rwxr--r-- 1 nobody blast 41492 Feb 27 22:15 ecoli.nt.nhr -rwxr--r-- 1 nobody blast 4864 Feb 27 22:15 ecoli.nt.nin -rwxr--r-- 1 nobody blast 3200 Feb 27 22:15 ecoli.nt.nnd -rwxr--r-- 1 nobody blast 60 Feb 27 22:15 ecoli.nt.nni -rwxr--r-- 1 nobody blast 58320 Feb 27 22:15 ecoli.nt.nsd -rwxr--r-- 1 nobody blast 1264 Feb 27 22:15 ecoli.nt.nsi -rwxr--r-- 1 nobody blast 1165813 Feb 27 22:15 ecoli.nt.nsq When I run dbiblast command, there are some errors: # dbiblast Index a BLAST database Database name: ecoli Database directory [.]: Wildcard database filename [ecoli]: ecoli.* Release number [0.0]: Index date [00/00/00]: 07/08/02 N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 640: cannot open ./ecoli.nt.nhr table file ./ecoli.nt.nhr.nin Does anybody have some ideas? Thank you very much in advance. Grace From David.Bauer at SCHERING.DE Tue Jul 9 06:00:22 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 9 Jul 2002 08:00:22 +0200 Subject: Antwort: Message-ID: Hi Qingjuan, I know this problem. dbiblast expects to find the source fasta file which was used for formating the BLAST databases in the same directory. The 'Wildcard database filename' is used as base and then the .nin etc. are appended to this name. So the error says that dbiblast thinks 'ecoli.nt.nhr' is the fasta file and looks for a BLAST index file 'ecoli.nt.nhr.nin'. Either copy the fasta file in the same directory or create a symbolic link there. Then specify "ecoli.nt" as "Wildcard database filename" which in this case is not a wildcard. Peter, what about changing "Wildcard database filename" to "Filename of fasta source file" in dbiblast ? David. Hi, I am configuring emboss for blast database. I copied part of database from balst formatted database into my test directory. Here is the files: # ls -l total 1308 -rwxr--r-- 1 root system 11306 Jul 8 13:52 alu.n.nhr -rwxr--r-- 1 root system 3988 Jul 8 13:52 alu.n.nin -rwxr--r-- 1 root system 16640 Jul 8 13:52 alu.n.nsd -rwxr--r-- 1 root system 411 Jul 8 13:52 alu.n.nsi -rwxr--r-- 1 root system 20336 Jul 8 13:52 alu.n.nsq -rwxr--r-- 1 nobody blast 41492 Feb 27 22:15 ecoli.nt.nhr -rwxr--r-- 1 nobody blast 4864 Feb 27 22:15 ecoli.nt.nin -rwxr--r-- 1 nobody blast 3200 Feb 27 22:15 ecoli.nt.nnd -rwxr--r-- 1 nobody blast 60 Feb 27 22:15 ecoli.nt.nni -rwxr--r-- 1 nobody blast 58320 Feb 27 22:15 ecoli.nt.nsd -rwxr--r-- 1 nobody blast 1264 Feb 27 22:15 ecoli.nt.nsi -rwxr--r-- 1 nobody blast 1165813 Feb 27 22:15 ecoli.nt.nsq When I run dbiblast command, there are some errors: # dbiblast Index a BLAST database Database name: ecoli Database directory [.]: Wildcard database filename [ecoli]: ecoli.* Release number [0.0]: Index date [00/00/00]: 07/08/02 N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 640: cannot open ./ecoli.nt.nhr table file ./ecoli.nt.nhr.nin Does anybody have some ideas? Thank you very much in advance. Grace From ekolomiets at yahoo.com Tue Jul 9 16:47:23 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Tue, 9 Jul 2002 09:47:23 -0700 (PDT) Subject: EMBOSS Qs Message-ID: <20020709164723.27018.qmail@web13808.mail.yahoo.com> Hello, What can be wrong if my MSE from BMBASSY can not compile? I downloaded it and try to do make/make install/ and I am getting arrors like that: (attachment) Also there are processes running: re root 1077 0.0 0.9 81268 7668 ? S 12:22 0:00 /usr/sbin/httpd -DHAVE_ACCESS -DHAVE_PROXY -DHAVE_AUTH_ANON -DHAVE_AC apache 1119 0.0 1.0 81368 7884 ? S 12:22 0:00 /usr/sbin/httpd -DHAVE_ACCESS -DHAVE_PROXY -DHAVE_AUTH_ANON -DHAVE_AC Another question about database specifications. I created EMBOSS_DATA directory in /usr/local/EMBOSS-2.4.1/EMBOSS_DATA and in emboss.defaults uncommented embl, gb, and some other databases, but EMBOSS still use data only from test databases tembl, tgb and so on. Showdb - have all databases (test and newly added in a list). What other changes to emboss.defaults should i make? Thanks for your time! Elena Kolomiets Research Assistant Department of Plant Pathology Texas A&M University __________________________________________________ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: MSE-Errors Type: application/octet-stream Size: 2856 bytes Desc: MSE-Errors URL: From qingjuan at wistar.upenn.edu Tue Jul 9 18:54:00 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 9 Jul 2002 14:54:00 -0400 Subject: dbiblast with newest blast database Message-ID: <200207091454.AA65470682@wistar.upenn.edu> Hi, I am configuring emboss with blast database. Because blast database upgrade new format since Feb., this year. the dbiblast can not support *.nal and *msk file extension. Does anybody have similar experience, and tell me how to make index with 'dbiblast' for blast database. Thank you very mcuh Grace From qingjuan at wistar.upenn.edu Tue Jul 9 21:34:28 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 9 Jul 2002 17:34:28 -0400 Subject: dbiblast command Message-ID: <200207091734.AA272367818@wistar.upenn.edu> Hi, When I use dbiblast command for chromosome database : # ls -l chromo* -rwx------ 1 root system 264482 Jul 9 17:28 chromosome.nhr -rwx------ 1 root system 24464 Jul 9 17:28 chromosome.nin -rwx------ 1 root system 16248 Jul 9 17:28 chromosome.nnd -rwx------ 1 root system 108 Jul 9 17:28 chromosome.nni -rwx------ 1 root system 178637 Jul 9 17:28 chromosome.nsd -rwx------ 1 root system 4092 Jul 9 17:28 chromosome.nsi -rwx------ 1 root system 134588104 Jul 9 17:28 chromosome.nsq -rwx------ 1 root system 84008 Jul 9 17:28 chromosome.ntd -rwx------ 1 root system 12368 Jul 9 17:28 chromosome.nti # dbiblast Index a BLAST database Database name: chromo Database directory [.]: Wildcard database filename [chromo]: chromosome.nin Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 547: failed to parse ' # Does anybody have ideas? what should I input for 'Wildcard databse filename' question? Thank you very much. Grace From cquijano at iib.uam.es Fri Jul 19 08:30:06 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Fri, 19 Jul 2002 10:30:06 +0200 Subject: eseqboot: Format problems Message-ID: <3D37CE0E.6020407@iib.uam.es> Hello, We are using eseqboot with all known formats, but by no way are we able to make it run fine. The information below is which w2h drops using FASTA format, and it appears to be an invalid format problem. First of all sorry if we are not using the correct input file type. But after reading de doc it seems clear that what eseqboot expects is an alignment input file. Does anybody know how to run it properly?* Thanks. Name*: /eseqboot/ *Started*: 02-07-19 10:01:56 *With Init file*: .. -datafile=lmb_2495.fasta -method=Seq -test=Boot -outfile=/home/cquijano/data/diskette/eseqboot_3574.outfile !embosstext --- end of init file : 02-07-19 10:01:56 *Exit*: 255 emboss: eseqboot -datafile=lmb_2495.fasta -method=Seq -test=Boot -outfile=/home/cquijano/data/diskette/eseqboot_3574.outfile -auto BAD OPTION CHARACTER: > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbxlh at nottingham.ac.uk Tue Jul 23 08:50:31 2002 From: mbxlh at nottingham.ac.uk (Louise Honeyman) Date: Tue, 23 Jul 2002 09:50:31 +0100 Subject: Hi! Message-ID: Hi! I am wanting to use eprimer3 to design probes for in-situ hybridisation. I first need a pair of primers although the system will only allow mw to design a product of 200bp - I would ideally like something in the region of 400bp. Is there a way to change the settings to allow such? Also is there way to change the length of primers from 20bp? Thanks, Louise -------------- next part -------------- An HTML attachment was scrubbed... URL: From sabino at area.ba.cnr.it Tue Jul 23 15:46:27 2002 From: sabino at area.ba.cnr.it (Liuni Sabino) Date: Tue, 23 Jul 2002 17:46:27 +0200 Subject: Help on emowse program Message-ID: <5.0.2.1.0.20020723174019.02397da0@194.119.200.100> Hi, I have building a database of protein sequences with dbifasta named orf. I have execute the program emowse (see below) % emowse Protein identification by mass spectrometry Input sequence(s): orf:* Input file: peptides.txt Whole sequence molwt [0]: Output file [pp000001.emowse]: Floating exception (core dumped) and the program exit for core dump. My input file is: 745.4311 752.4110 797.3966 839.1514 929.8979 982.4935 1091.6398 1116.7359 1199.7238 1232.6318 1260.6841 1278.8252 1307.6915 1320.7267 1345.6921 1513.7327 1627.9873 1683.8895 1716.2595 1829.0047 1887.8467 1951.9813 2023.3943 Any help for this problem. Thanks in advance Sabino Liuni ----------------------------------------------------- Bioinformatics and Genomic Group - C.N.R. Italian EMBnet Node Via Amendola 166/5 - 70126 Bari (Italy) Tel. +39-80-5482130 - Fax. +39-80-5482607 e_mail:sabino at area.ba.cnr.it -------------- next part -------------- An HTML attachment was scrubbed... URL: From ableasby at hgmp.mrc.ac.uk Tue Jul 23 16:01:07 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 23 Jul 2002 17:01:07 +0100 (BST) Subject: Help on emowse program Message-ID: <200207231601.RAA08191@bromine.hgmp.mrc.ac.uk> Sabino, Co-incidentally I am rewriting the successor to emowse at the moment (our Unit has recently purchased a mass spectrometer allowing the code to be tested first hand). I will look at your emowse problem. Alan From cbonnard at isrec-sg1.unil.ch Wed Jul 24 07:32:01 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 09:32:01 +0200 Subject: Interactive commands Message-ID: <10207240932.ZM4264@isrec-sg1> Hello, Any idea of the place to search for this problem? % dbiflat tsw EMBOSS An error in dbiflat.c at line 194: No files selected % I cannot find a way to get into any interactivity with (at least) this utility. Somehow frustrating.. Thanks for your advice, Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From David.Bauer at SCHERING.DE Wed Jul 24 07:44:59 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jul 2002 09:44:59 +0200 Subject: Antwort: Interactive commands Message-ID: Hi, just "dbiflat" without ANY paramter brings you in interactive mode. With "dbiflat -help" you get an overview of all options. And "tfm dbiflat" gives a more detailed explanation about the program. Hope this helps, David. Hello, Any idea of the place to search for this problem? % dbiflat tsw EMBOSS An error in dbiflat.c at line 194: No files selected % I cannot find a way to get into any interactivity with (at least) this utility. Somehow frustrating.. Thanks for your advice, Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From simon.andrews at bbsrc.ac.uk Wed Jul 24 07:49:36 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Wed, 24 Jul 2002 08:49:36 +0100 Subject: Interactive commands Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> > -----Original Message----- > From: cbonnard at isrec-sg1.unil.ch > Subject: Interactive commands > > > Hello, > > Any idea of the place to search for this problem? > > % dbiflat tsw > > EMBOSS An error in dbiflat.c at line 194: > No files selected > > I cannot find a way to get into any interactivity with (at > least) this utility. Hmmm. On my system: $ uname -sr Linux 2.4.9-21smp $ embossversion Writes the current EMBOSS version number 2.4.1 $ dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ Entry format [SWISS]: ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. Simon. From cbonnard at isrec-sg1.unil.ch Wed Jul 24 08:03:19 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 10:03:19 +0200 Subject: Interactive commands In-Reply-To: "simon andrews (BI)" "RE: Interactive commands" (Jul 24, 8:49am) References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <10207241003.ZM4334@isrec-sg1> Don't know what to say: the compilation went perfectly OK (as far as error messages...) $ uname -sr SunOS 5.8 % embossversion 2.4.1 %dbiflat Error: Too short (dbname) - minimum length is 1 characters %checktrans it hangs untill a CTRL-C 8-( >>>>> YES, obviously a config problem..but which ? I think that I will need some clue.. Thanks a lot! On Jul 24, 8:49am, simon andrews (BI) wrote: > Subject: RE: Interactive commands > > -----Original Message----- > > From: cbonnard at isrec-sg1.unil.ch > > Subject: Interactive commands > > > > > > Hello, > > > > Any idea of the place to search for this problem? > > > > % dbiflat tsw > > > > EMBOSS An error in dbiflat.c at line 194: > > No files selected > > > > I cannot find a way to get into any interactivity with (at > > least) this utility. > > Hmmm. On my system: > > $ uname -sr > Linux 2.4.9-21smp > > $ embossversion > Writes the current EMBOSS version number > 2.4.1 > > $ dbiflat > Index a flat file database > EMBL : EMBL > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > GB : Genbank, DDBJ > Entry format [SWISS]: > > ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. > > Simon. >-- End of excerpt from simon andrews (BI) -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From peter.rice at uk.lionbioscience.com Wed Jul 24 08:08:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Jul 2002 09:08:09 +0100 Subject: Interactive commands References: <10207240932.ZM4264@isrec-sg1> Message-ID: <3D3E6069.CE665EE4@uk.lionbioscience.com> Claude Bonnard wrote: > Any idea of the place to search for this problem? > % dbiflat tsw > EMBOSS An error in dbiflat.c at line 194: > No files selected > % > I cannot find a way to get into any interactivity with (at least) this utility. You can turn off the interactivity, but only for all applications (did you try any others?), if you try (csh): % setenv EMBOSS_FILTER Y or % setenv EMBOSS_AUTO Y (or if you have emboss_filter or emboss_auto defined in your emboss.defaults or ~/.embossrc files) These are just ways to put -filter or -auto on the command line for every application. You can hunt for them with -noauto or -nofilter on the command line to see whether these are causing your problem. The only parameter (no qualifier needed on the command line) for dbiflat is the database name. Everything else will be prompted for. OZE :-) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Wed Jul 24 08:20:14 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 24 Jul 2002 10:20:14 +0200 Subject: Interactive commands Message-ID: I'm running the 2.4.1 on SunOS 5.7 and it works perfectly. Probably this is a 5.8 specific issue. Hope someone with the same OS version can give you a hint. I have no idea... :--| Good luck! David Don't know what to say: the compilation went perfectly OK (as far as error messages...) $ uname -sr SunOS 5.8 % embossversion 2.4.1 %dbiflat Error: Too short (dbname) - minimum length is 1 characters %checktrans it hangs untill a CTRL-C 8-( >>>>> YES, obviously a config problem..but which ? I think that I will need some clue.. Thanks a lot! On Jul 24, 8:49am, simon andrews (BI) wrote: > Subject: RE: Interactive commands > > -----Original Message----- > > From: cbonnard at isrec-sg1.unil.ch > > Subject: Interactive commands > > > > > > Hello, > > > > Any idea of the place to search for this problem? > > > > % dbiflat tsw > > > > EMBOSS An error in dbiflat.c at line 194: > > No files selected > > > > I cannot find a way to get into any interactivity with (at > > least) this utility. > > Hmmm. On my system: > > $ uname -sr > Linux 2.4.9-21smp > > $ embossversion > Writes the current EMBOSS version number > 2.4.1 > > $ dbiflat > Index a flat file database > EMBL : EMBL > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > GB : Genbank, DDBJ > Entry format [SWISS]: > > ..and it's all interactive from there on. Are you using an old Emboss version? If not there might be a problem with your installation. > > Simon. >-- End of excerpt from simon andrews (BI) -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From gwilliam at hgmp.mrc.ac.uk Wed Jul 24 08:25:54 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 24 Jul 2002 09:25:54 +0100 Subject: Interactive commands References: Message-ID: <3D3E6492.F2B76B92@hgmp.mrc.ac.uk> It works for me under 5.8: % uname -a SunOS californium 5.8 Generic_108528-11 sun4u sparc SUNW,Ultra-5_10 % dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ Entry format [SWISS]: Gary David.Bauer at SCHERING.DE wrote: > > I'm running the 2.4.1 on SunOS 5.7 and it works perfectly. > Probably this is a 5.8 specific issue. Hope someone with the same OS version can > give you a hint. > I have no idea... :--| > > Good luck! > David > > Don't know what to say: the compilation went perfectly OK (as far as error > messages...) > > $ uname -sr > SunOS 5.8 > % embossversion > 2.4.1 > %dbiflat > Error: Too short (dbname) - minimum length is 1 characters > %checktrans > > it hangs untill a CTRL-C 8-( > > >>>>> YES, obviously a config problem..but which ? > > I think that I will need some clue.. > > Thanks a lot! > > On Jul 24, 8:49am, simon andrews (BI) wrote: > > Subject: RE: Interactive commands > > > -----Original Message----- > > > From: cbonnard at isrec-sg1.unil.ch > > > Subject: Interactive commands > > > > > > > > > Hello, > > > > > > Any idea of the place to search for this problem? > > > > > > % dbiflat tsw > > > > > > EMBOSS An error in dbiflat.c at line 194: > > > No files selected > > > > > > I cannot find a way to get into any interactivity with (at > > > least) this utility. > > > > Hmmm. On my system: > > > > $ uname -sr > > Linux 2.4.9-21smp > > > > $ embossversion > > Writes the current EMBOSS version number > > 2.4.1 > > > > $ dbiflat > > Index a flat file database > > EMBL : EMBL > > SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew > > GB : Genbank, DDBJ > > Entry format [SWISS]: > > > > ..and it's all interactive from there on. Are you using an old Emboss > version? If not there might be a problem with your installation. > > > > Simon. > >-- End of excerpt from simon andrews (BI) > > -- > Claude Bonnard Ph.D. > ISREC (Swiss Institute for Experimental Cancer Research) > Bioinformatics Group > Ch des Boveresses 155 > CH-1066 Epalinges > Switzerland > phone: [41-21]-692-5891/-2236 > fax: [41-21]-652-6933 -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Wed Jul 24 08:34:53 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Jul 2002 09:34:53 +0100 Subject: Interactive commands References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> <10207241003.ZM4334@isrec-sg1> Message-ID: <3D3E66AD.56D20FC3@uk.lionbioscience.com> Claude Bonnard wrote: > > %checktrans > > it hangs untill a CTRL-C 8-( > > >>>>> YES, obviously a config problem..but which ? > > I think that I will need some clue.. That's a big clue. % checktrans -auto Error: Unable to read sequence '' % checktrans -filter ... hangs until you hit control-C ... or control-D ... because it is now defaulting to read standard input. Control-C will stop it, Control-D will say "Error: Unable to read sequence 'stdin'" Try: % checktrans -nofilter If that works, then look for an EMBOSS_FILTER definition somewhere. HTH Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From cbonnard at isrec-sg1.unil.ch Wed Jul 24 09:22:26 2002 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Wed, 24 Jul 2002 11:22:26 +0200 Subject: Interactive commands In-Reply-To: Peter Rice "Re: Interactive commands" (Jul 24, 9:34am) References: <2DC41140A89ED411989D00508BDCD9ED01E28651@bi-exsrv1.iapc.bbsrc.ac.uk> <10207241003.ZM4334@isrec-sg1> <3D3E66AD.56D20FC3@uk.lionbioscience.com> Message-ID: <10207241122.ZM4512@isrec-sg1> Thanks a lot, Peter! This was -for an unknown reason the emboss.default which contained: set emboss_filter 1 removing it solved this . Thanks also to all of you for your very fast replies! Regards, Claude On Jul 24, 9:34am, Peter Rice wrote: > Subject: Re: Interactive commands > Claude Bonnard wrote: > > > > %checktrans > > > > it hangs untill a CTRL-C 8-( > > > > >>>>> YES, obviously a config problem..but which ? > > > > I think that I will need some clue.. > > That's a big clue. > > % checktrans -auto > Error: Unable to read sequence '' > > % checktrans -filter > ... hangs until you hit control-C ... or control-D ... because it is now > defaulting to read standard input. > > Control-C will stop it, Control-D will say "Error: Unable to read sequence > 'stdin'" > > Try: > > % checktrans -nofilter > > If that works, then look for an EMBOSS_FILTER definition somewhere. > > HTH > > Peter > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 >-- End of excerpt from Peter Rice -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891/-2236 fax: [41-21]-652-6933 From c_sanjib1 at rediffmail.com Thu Jul 25 12:40:36 2002 From: c_sanjib1 at rediffmail.com (Sanjib Chatterjee) Date: 25 Jul 2002 12:40:36 -0000 Subject: No subject Message-ID: <20020725124036.25980.qmail@mailFA11.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From peter.rice at uk.lionbioscience.com Thu Jul 25 15:45:14 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 25 Jul 2002 16:45:14 +0100 Subject: References: <20020725124036.25980.qmail@mailFA11.rediffmail.com> Message-ID: <3D401D0A.9A069042@uk.lionbioscience.com> Sanjib Chatterjee wrote: > > sir, > I want to know whether I can run the programme > "cpgreport" for a sequence of length 50 MB. Yes! EMBOSS will read any sequence length, it is limited by the memory on the machine. By default, EMBOSS reads the input sequence into a buffer while gussing the format. If you specify the format in the USA or on the command line it will use less memory for a very large sequence. For example: % cpgreport fasta::big.seq % cpgreport big.seq -sf fasta regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From qingjuan at wistar.upenn.edu Thu Jul 25 16:17:08 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Thu, 25 Jul 2002 12:17:08 -0400 Subject: dbiblast Message-ID: <200207251217.AA95682752@wistar.upenn.edu> >The answer is that you should use 'chromosome' as the wildcard >database name. Secondly, the author of dbiblast thinks there >might be some problems with the 2.4.1 version and this will >be corrected in 2.5.0 which is out soon. Thirdly, do not use >the very latest formatdb (NCBI have not yet released the >details of their index format so EMBOSS cannot index them). I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. I follow you instruction, it failed also. Here is the interactive result: # ls -l total 434903 -rwxr--r-- 1 nobody blast 76626843 Jul 4 22:09 patnt.nhr -rwxr--r-- 1 nobody blast 8066892 Jul 4 22:19 patnt.nin -rwxr--r-- 1 nobody blast 5377840 Jul 4 22:10 patnt.nnd -rwxr--r-- 1 nobody blast 21052 Jul 4 22:10 patnt.nni -rwxr--r-- 1 nobody blast 142820076 Jul 4 22:13 patnt.nsd -rwxr--r-- 1 nobody blast 2926655 Jul 4 22:19 patnt.nsi -rwxr--r-- 1 nobody blast 92506630 Jul 4 22:19 patnt.nsq -rwxr--r-- 1 nobody blast 119501 Jul 4 22:19 patnt.ntd -rwxr--r-- 1 nobody blast 17904 Jul 4 22:19 patnt.nti -rwxr--r-- 1 nobody blast 116819853 Jun 28 09:30 patnt.tar.gz # # dbiblast Index a BLAST database Database name: patnt Database directory [.]: Wildcard database filename [patnt]: patnt Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: N 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 EMBOSS An error in dbiblast.c at line 333: No files selected # if i use patnt.nin in 'wildcard databse filename', that works without complain. but when I use seqret or other command to search the sequence, there are always error message: # ls -l total 435242 -rwxr-xr-x 1 root system 416 Jul 25 10:58 acnum.hit -rwxr-xr-x 1 root system 742 Jul 25 10:58 acnum.trg -rwxr-xr-x 1 root system 322 Jul 25 10:56 division.lkp -rwxr-xr-x 1 root system 338334 Jul 25 10:58 entrynam.idx -rwxr--r-- 1 nobody blast 76626843 Jul 4 22:09 patnt.nhr -rwxr--r-- 1 nobody blast 8066892 Jul 4 22:19 patnt.nin -rwxr--r-- 1 nobody blast 5377840 Jul 4 22:10 patnt.nnd -rwxr--r-- 1 nobody blast 21052 Jul 4 22:10 patnt.nni -rwxr--r-- 1 nobody blast 142820076 Jul 4 22:13 patnt.nsd -rwxr--r-- 1 nobody blast 2926655 Jul 4 22:19 patnt.nsi -rwxr--r-- 1 nobody blast 92506630 Jul 4 22:19 patnt.nsq -rwxr--r-- 1 nobody blast 119501 Jul 4 22:19 patnt.ntd -rwxr--r-- 1 nobody blast 17904 Jul 4 22:19 patnt.nti -rwxr--r-- 1 nobody blast 116819853 Jun 28 09:30 patnt.tar.gz # seqret Reads and writes (returns) sequences Input sequence(s): patnt:E00007.1 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:E00007.1' Input sequence(s): patnt:E00007 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:E00007' # seqret Reads and writes (returns) sequences Input sequence(s): patnt:2168318 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:2168318' Input sequence(s): patnt:2168314 Error: BLAST Entry failed Error: Unable to read sequence 'patnt:2168314' # In my emboss.default: DB patnt [ type: N method: blast format: ncbi dir: /db4/users/qgu/test/test_dbi file: patnt.* indexdir: /db4/users/qgu/test/test_dbi release: "1.0" comment: "patnt formatted database --BLAST NCBI" ] Also, my fasta and genbank files works fine, only blast database can not work well. Your help will be highly appreciated. Grace From peter.rice at uk.lionbioscience.com Thu Jul 25 16:39:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 25 Jul 2002 17:39:09 +0100 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> Message-ID: <3D4029AD.23285B37@uk.lionbioscience.com> Qingjuan Gu (Grace) wrote: > > >Thirdly, do not use > >the very latest formatdb (NCBI have not yet released the > >details of their index format so EMBOSS cannot index them). > > I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. NCBI have changed the format of blast databases to "ASN.1 headers" (also known as 'format version 4') If you FTP the databases from NCBI you will probably get them in this format. We have asked NCBI for a description of the format. They promised to send one. Until then, the new blast format is not supported. I checked the latest code for the FASTA package, which has the same problem. Has anyone figured out how to decode this new blast database format yet? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Thu Jul 25 16:43:35 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Thu, 25 Jul 2002 18:43:35 +0200 Subject: dbiblast In-Reply-To: <200207251217.AA95682752@wistar.upenn.edu> References: <200207251217.AA95682752@wistar.upenn.edu> Message-ID: <20020725164335.GA3727@moulinette.dyndns.org> > # dbiblast > Index a BLAST database > Database name: patnt > Database directory [.]: > Wildcard database filename [patnt]: patnt I think the problem is that you are trying to format an already formatted database. You should get the flat file and format it instead. Charles From asen.nenov at metalife.de Thu Jul 25 19:35:36 2002 From: asen.nenov at metalife.de (Asen Nenov) Date: Thu, 25 Jul 2002 21:35:36 +0200 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> <3D4029AD.23285B37@uk.lionbioscience.com> Message-ID: <3D405308.5030709@metalife.de> I wish to suggest a way of understanding the BLAST asn format.. Of course this is last hope method. :-) Use the converters asn->xml of NCBI and do something with the output. Then reversibly reconstruct the data format. Enjoy. Regards Asen Nenov Peter Rice wrote: > Qingjuan Gu (Grace) wrote: > >>>Thirdly, do not use >>>the very latest formatdb (NCBI have not yet released the >>>details of their index format so EMBOSS cannot index them). >>> >>I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. >> > > NCBI have changed the format of blast databases to "ASN.1 headers" (also > known as 'format version 4') > > If you FTP the databases from NCBI you will probably get them in this > format. > > We have asked NCBI for a description of the format. They promised to send > one. > Until then, the new blast format is not supported. > > I checked the latest code for the FASTA package, which has the same > problem. > > Has anyone figured out how to decode this new blast database format yet? > > regards, > > Peter Rice > > -- Best Regards Asen Nenov METALIFE AG asen.nenov at metalife.de www.metalife.de From peter.rice at uk.lionbioscience.com Fri Jul 26 10:48:50 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 26 Jul 2002 11:48:50 +0100 Subject: dbiblast References: <200207251217.AA95682752@wistar.upenn.edu> <3D4029AD.23285B37@uk.lionbioscience.com> <3D405308.5030709@metalife.de> Message-ID: <3D412912.4A934BF1@uk.lionbioscience.com> Asen Nenov wrote: > > I wish to suggest a way of understanding the BLAST asn format.. Of > course this is last hope method. :-) > Use the converters asn->xml of NCBI and do something with the output. > Then reversibly reconstruct the data format. Enjoy. Unfortunately ... the blast databases have a *binary* format. No way to convert this into ASN.1 (which EMBOSS could probably parse more easily than XML). I suppose reading the formatdb source code might help .... but it would really help if NCBI could document their format. I'm sure they know other software (EMBOSS, fasta, and others) is reading blast database files. regards, Peter From sebastian.bassi at ar.advantaseeds.com Mon Jul 29 08:29:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Mon, 29 Jul 2002 10:29:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A954514D59@e2knl1.nl.seedsnetwork.com> Hi, I?ve found 2 problems with EMBOSS. I?ve installed this in the past under Solaris 7 (Sun) and several flavors of Linux. Now I?m trying to compile it under Red Hat 6.2 server. The configure stage goes by OK, but when I try to compile I get: gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_ STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.4.1\" -D STDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE _STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDI NT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H= 1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_U NISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FOR K=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DX_DISPLAY_MISSING=1 -DHAVE_LIBM=1 -I. - I. -I../nucleus -I../ajax -I../plplot -I/usr/local -DNO_AUTH -g -O2 -c `test - f 'abiview.c' || echo './'`abiview.c /bin/sh ../libtool --mode=link gcc -g -O2 -o abiview abiview.o ../nucleus/li bnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -lX11 -lm mkdir .libs gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.l ibs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -lX11 -lm -Wl,--rpath -Wl,/usr/local/lib /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[2]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make: *** [all-recursive] Error 1 [root at pescadilla EMBOSS-2.4.1]# Perhaps it?s something related to graphics, since is a server machine, X is not installed. Is X needed in order to compile it? I really need to use only text based programs from EMBOSS. If there?s a program witch needs X, I would like not to compile it but keep on working with the command line (CL) ones. Now, it seems that I can?t compile even CL programs because I don?t have X installed. Maybe I?m wrong. I also reporting that EMNU program is not where the EMBASSY web page states it is: ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.4.tar.gz -------------- next part -------------- An HTML attachment was scrubbed... URL: From jcurole at cisunix.unh.edu Mon Jul 29 15:07:02 2002 From: jcurole at cisunix.unh.edu (Jason Curole) Date: Mon, 29 Jul 2002 11:07:02 -0400 Subject: Compiling EMBOSS 2.4.1 on Mac OS X Message-ID: Dear users, I am trying to compile the EMBOSS 2.4.1 package on OS X. I have installed X Darwin and this runs okay. I run configure and that also seem to run okay. I then make and it runs for a while but eventually bombs out on the error make[3]: *** No rule to make target `alignment_differences_group.html',. The last few lines of terminal text prior to the fail are pasted in below. I appreciate any help anyone could provide. Thanks, Jason Making install in wormpep make[3]: Nothing to be done for `install-exec-am'. /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/test/wormpep mkdir /usr/local/share/EMBOSS/test/wormpep /usr/bin/install -c -m 644 wormpep /usr/local/share/EMBOSS/test/wormpep/wormpep /usr/bin/install -c -m 644 acnum.hit /usr/local/share/EMBOSS/test/wormpep/acnum.hit /usr/bin/install -c -m 644 acnum.trg /usr/local/share/EMBOSS/test/wormpep/acnum.trg /usr/bin/install -c -m 644 division.lkp /usr/local/share/EMBOSS/test/wormpep/division.lkp /usr/bin/install -c -m 644 entrynam.idx /usr/local/share/EMBOSS/test/wormpep/entrynam.idx /usr/bin/install -c -m 644 des.hit /usr/local/share/EMBOSS/test/wormpep/des.hit /usr/bin/install -c -m 644 des.trg /usr/local/share/EMBOSS/test/wormpep/des.trg make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. Making install in doc Making install in manuals make[3]: Nothing to be done for `install-exec-am'. /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/doc/manuals mkdir /usr/local/share/EMBOSS/doc mkdir /usr/local/share/EMBOSS/doc/manuals /usr/bin/install -c -m 644 admin.sty /usr/local/share/EMBOSS/doc/manuals/admin.sty /usr/bin/install -c -m 644 admin.tex /usr/local/share/EMBOSS/doc/manuals/admin.tex /usr/bin/install -c -m 644 admin.aux /usr/local/share/EMBOSS/doc/manuals/admin.aux /usr/bin/install -c -m 644 admin.dvi /usr/local/share/EMBOSS/doc/manuals/admin.dvi /usr/bin/install -c -m 644 admin.log /usr/local/share/EMBOSS/doc/manuals/admin.log /usr/bin/install -c -m 644 admin.pdf /usr/local/share/EMBOSS/doc/manuals/admin.pdf /usr/bin/install -c -m 644 admin.ps /usr/local/share/EMBOSS/doc/manuals/admin.ps /usr/bin/install -c -m 644 admin.toc /usr/local/share/EMBOSS/doc/manuals/admin.toc /usr/bin/install -c -m 644 adminguide.tar.gz /usr/local/share/EMBOSS/doc/manuals/adminguide.tar.gz /usr/bin/install -c -m 644 program.ps.gz /usr/local/share/EMBOSS/doc/manuals/program.ps.gz /usr/bin/install -c -m 644 EMBOSS-FreeBSD-HOWTO.txt /usr/local/share/EMBOSS/doc/manuals/EMBOSS-FreeBSD-HOWTO.txt /usr/bin/install -c -m 644 emboss_qg.pdf /usr/local/share/EMBOSS/doc/manuals/emboss_qg.pdf /usr/bin/install -c -m 644 emboss_qg.ps /usr/local/share/EMBOSS/doc/manuals/emboss_qg.ps Making install in programs Making install in html make[3]: *** No rule to make target `alignment_differences_group.html', needed by `all-am'. Stop. make[2]: *** [install-recursive] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [install-recursive] Error 1 Jason P. Curole Hubbard Center for Genome Studies and Program in Genetics Genomics I ETB 35 Colovos Road University of New Hampshire Durham NH 03824-3534 http://tilapia.unh.edu/WWWPages/curole/curole.html From sebastian.bassi at ar.advantaseeds.com Mon Jul 29 13:38:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Mon, 29 Jul 2002 15:38:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A9544F6E4E@e2knl1.nl.seedsnetwork.com> ______________________________ Forward Header __________________________________ Subject: Re[2]: Instalation and D'd problem. Author: Sebastian Bassi at MOBILE-KAPELLE Date: 7/29/2002 3:31 PM Hello, After trying the "wihout x" option, I?ve got the same error. I did: # ./configure --without-x --x-includes="" --x-libraries="" (before that I did a "make clean" in order to start againg). Then, after the make command I got: [a lot output deleted] gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.l ibs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -lX11 -lm -Wl,--rpath -Wl,/usr/local/lib /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 make[2]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/sbassi/EMBOSS-2.4.1/emboss' make: *** [all-recursive] Error 1 [root at pescadilla EMBOSS-2.4.1]# ______________________________ Reply Separator _________________________________ Subject: Re: Instalation and D'd problem. Author: "ableasby at hgmp.mrc.ac.uk" at exkapelle Date: 7/29/2002 4:08 PM Thanks for the EMNU information. As far as X11 goes it is a known problem and is on the list of things to do. Please try configuring with: --without-x --x-includes="" --x-libraries="" and let me know if that solves it for you. Rgds Alan Bleasby HGMP -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Forward.txt URL: From rgrams at alpha.tu.ac.th Tue Jul 30 06:52:20 2002 From: rgrams at alpha.tu.ac.th (Rudi Grams) Date: Tue, 30 Jul 2002 13:52:20 +0700 Subject: Compiling EMBOSS 2.4.1 on Mac OS X Message-ID: <3D44B0C4@email.tu.ac.th> Any chance that you used stuffit expander to extract the emboss archive? Stuffit cannot deal with long file names and will change the names of such files! alignment_differences_group.html and others of the html files exceed the name length that stuffit can handle. Better use the unix tools as described in the manual. By the way I'am working on a simple GUI for emboss apps done in AppleScript Studio, similar to the Linux/Kaptain interface by Thomas Siegmund. If there is any interest please let me know... Kindly, Rudi Rudi Grams Faculty of Allied Health Sciences Thammasat University Rangsit Campus Pathum Thani 12121 Thailand From abrown at nimr.mrc.ac.uk Tue Jul 30 13:36:27 2002 From: abrown at nimr.mrc.ac.uk (Alex Brown) Date: Tue, 30 Jul 2002 14:36:27 +0100 Subject: Some help required. Message-ID: <5911EB42-A3C1-11D6-B96B-0003938768AC@nimr.mrc.ac.uk> Hi. Firstly, let me apologize for what may seem a trivial problem, but I have nowhere else to turn. I have 'used' UNIX previously, but only as a user (and not very often at that), and not as an administrator, and the problem is getting EMBOSS to function properly. I have installed EMBOSS on a Macintosh PowerBook G4, under Darwin. I am also running XDarwin (XFree86 4.2.0). After installation and running 'make install', 'wossname -auto | less' gives a long list of programs, as stated in the EMBOSS Administrators Guide, section 2.3.5. All the program files are located in the /usr/local/bin directory - I notice that there is no EMBOSS entries in /usr/share/man. Is this correct ? In order to get the 'showdb' command to list the available databases, I uncommented the first line of the emboss.default.template file (SET emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to emboss.default. The command 'showdb' results in the following output: # Name Type ID Qry All Comment # ==== ==== == === === ======= tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD-ROM index tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index indicating the databases in the /local/share/EMBOSS/test directory. So far so good. However, attempting to work through the tutorial on the EMBOSS web-site, I find that I am unable to access the databases: for example [xxxxxx:~] me% seqret Reads and writes (returns) sequences Input sequence(s): tembl:hs* Warning: Cannot open division file '' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hs*' Input sequence(s): I was assuming that the databases that came with the installation would work, and would allow me to work round to installing my own databases. The above would indicate that there is still something I have yet to do. Could someone please offer me some guidance on this. Many thanks. Alex Brown. From qingjuan at wistar.upenn.edu Tue Jul 30 14:27:36 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Tue, 30 Jul 2002 10:27:36 -0400 Subject: Some help required. Message-ID: <200207301027.AA112197860@wistar.upenn.edu> The possible reason for this: your 'real database' have permission problem, double-check your 'tembl' database mod. ---------- Original Message ---------------------------------- From: Alex Brown Date: Tue, 30 Jul 2002 14:36:27 +0100 >Hi. > >Firstly, let me apologize for what may seem a trivial problem, but I >have nowhere else to turn. I have 'used' UNIX previously, but only as a >user (and not very often at that), and not as an administrator, and the >problem is getting EMBOSS to function properly. > >I have installed EMBOSS on a Macintosh PowerBook G4, under Darwin. I am >also running XDarwin (XFree86 4.2.0). After installation and running >'make install', 'wossname -auto | less' gives a long list of programs, >as stated in the EMBOSS Administrators Guide, section 2.3.5. > >All the program files are located in the /usr/local/bin directory - I >notice that there is no EMBOSS entries in /usr/share/man. Is this >correct ? > >In order to get the 'showdb' command to list the available databases, I >uncommented the first line of the emboss.default.template file (SET >emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to >emboss.default. The command 'showdb' results in the following output: > ># Name Type ID Qry All Comment ># ==== ==== == === === ======= >tpir P OK OK OK PIR using NBRF access for 4 files >tsw P OK OK OK Swissprot native format with EMBL CD-ROM >index >tswnew P OK OK OK Swissnew as 3 files in native format with >EMBL CD-ROM index >twp P OK OK OK EMBL new in native format with EMBL >CD-ROM index >tembl N OK OK OK EMBL in native format with EMBL CD-ROM >index >tgb N OK - - Genbank IDs >tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM >index > >indicating the databases in the /local/share/EMBOSS/test directory. > >So far so good. > >However, attempting to work through the tutorial on the EMBOSS web-site, >I find that I am unable to access the databases: for example > >[xxxxxx:~] me% seqret >Reads and writes (returns) sequences >Input sequence(s): tembl:hs* >Warning: Cannot open division file '' >Warning: seqCdQry failed >Error: Unable to read sequence 'tembl:hs*' >Input sequence(s): > >I was assuming that the databases that came with the installation would >work, and would allow me to work round to installing my own databases. >The above would indicate that there is still something I have yet to do. >Could someone please offer me some guidance on this. > >Many thanks. > >Alex Brown. > > From peter.rice at uk.lionbioscience.com Tue Jul 30 15:00:06 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 30 Jul 2002 16:00:06 +0100 Subject: Some help required. References: <5911EB42-A3C1-11D6-B96B-0003938768AC@nimr.mrc.ac.uk> Message-ID: <3D46A9F6.C6296B06@uk.lionbioscience.com> Alex Brown wrote: > In order to get the 'showdb' command to list the available databases, I > uncommented the first line of the emboss.default.template file (SET > emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to > emboss.default. The command 'showdb' results in the following output: > > indicating the databases in the /local/share/EMBOSS/test directory. > > So far so good. > > However, attempting to work through the tutorial on the EMBOSS web-site, > I find that I am unable to access the databases: for example > > [xxxxxx:~] me% seqret > Reads and writes (returns) sequences > Input sequence(s): tembl:hs* > Warning: Cannot open division file '' > Warning: seqCdQry failed > Error: Unable to read sequence 'tembl:hs*' > Input sequence(s): First, I assume your emboss.default file has: SET emboss_tempdata /local/share/EMBOSS/test Next, you can try: seqret -debug This will write a file seqret.dbg where I would expect lines like this: directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*' ajFileNewIn '/local/share/EMBOSS/test/embl/division.lkp' ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp' This is the division file which it says cannot be opened. If you see what appears to be the right filename, check file (and directory) protection. If you see something else, it may give a clue to where the setup is wrong, or you can get help from emboss-bug at embnet.org regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From naofumi at mac.com Tue Jul 30 15:34:50 2002 From: naofumi at mac.com (Naofumi Kagami) Date: Wed, 31 Jul 2002 00:34:50 +0900 Subject: Compiling EMBOSS 2.4.1 on Mac OS X In-Reply-To: Message-ID: Hi Jason, I just solved that one today. I think that the problem lies with Stuffit Expander. If you look into EMBOSS-2.4.1/doc/programs/html after expanding the archive, you will notice that the file 'alignment_differences_group.html' is missing the final 'l' in '.html'. The makefile is looking for '`alignment_differences_group.html' but only finds '`alignment_differences_group.htm', so it sends out an error and quits. At least that's what I'm guessing. I'm no UNIX expert myself :-). I am guessing that Stuffit Expander is choking on long filenames (the legacy of Classic) since the truncation is occurring after the 30th letter. After adding the final 'l' to the filename, do a make once more. You'll find other errors that have to be solved in the same way. After doing this several times, make should finish without errors. Then you can make install. Hope this works for you. Naofumi Kagami On 2002.07.30, at 00:07, Jason Curole wrote: > . I run configure and that also seem to run okay. > I then make and it runs for a while but eventually bombs out on the > error > make[3]: *** No rule to make target `alignment_differences_group.html',. > The last few lines of terminal text prior to the fail are pasted in > below. > I appreciate any help anyone could provide. > > Thanks, Jason > > Making install in wormpep > make[3]: Nothing to be done for `install-exec-am'. > /bin/sh ../../mkinstalldirs /usr/local/share/EMBOSS/test/wormpep > mkdir /usr/local/share/EMBOS From abrown at nimr.mrc.ac.uk Tue Jul 30 15:56:13 2002 From: abrown at nimr.mrc.ac.uk (Alex Brown) Date: Tue, 30 Jul 2002 16:56:13 +0100 Subject: Some help required. In-Reply-To: <3D46A9F6.C6296B06@uk.lionbioscience.com> Message-ID: OUCH !! (just me kicking myself). Initially, the emboss.default file had the line: SET emboss_tempdata path_to_directory_$EMBOSS/test I had assumed thet 'path_to_directory_$EMBOSS was a variable holding the path. Apparently not so. I edited this line as you suggested: SET emboss_tempdata /local/share/EMBOSS/test but again this didn't solve the problem. However, changing it to: SET emboss_tempdata /usr/local/share/EMBOSS/test did work. That might have been the root of the problem (groan !!) Many thanks for all the replies. Alex Brown. On Tuesday, July 30, 2002, at 04:00 PM, Peter Rice wrote: > First, I assume your emboss.default file has: > > SET emboss_tempdata /local/share/EMBOSS/test > > Next, you can try: > > seqret -debug > > This will write a file seqret.dbg where I would expect lines like this: > > directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*' > ajFileNewIn '/local/share/EMBOSS/test/embl/division.lkp' > ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp' > > This is the division file which it says cannot be opened. > > If you see what appears to be the right filename, check file (and > directory) protection. > > If you see something else, it may give a clue to where the setup is > wrong, > or you can get help from emboss-bug at embnet.org > > regards, > > Peter Rice > > -- > ------------------------------------------------ > Peter Rice, LION Bioscience Ltd, Cambridge, UK > peter.rice at uk.lionbioscience.com +44 1223 224723 > From sebastian.bassi at ar.advantaseeds.com Wed Jul 31 07:36:00 2002 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Wed, 31 Jul 2002 09:36:00 +0200 Subject: Instalation and D'd problem. Message-ID: <2AE73E3601DA0E428E14535564F6A9544F9397@e2knl1.nl.seedsnetwork.com> Hi, I installed the rpm you point me and it works!!!! Here is a proposed question (and answer) for the EMBOSS FAQ (under INSTALLATION). Q) Is there a way to install EMBOSS without X? (like in a text only server machine) A) Yes, you only need to install XFree86-devel package before configuring and compiling EMBOSS. (tried on a Red Hat 6.2 server installation). Thank you for your help.- PS: I?ll make a copy of this mail to the mailing list since it could help somebody else. ______________________________ Reply Separator _________________________________ Subject: RE: Instalation and D'd problem. Author: "ableasby at hgmp.mrc.ac.uk" at exkapelle Date: 7/31/2002 1:39 AM btw: I have been assuming all along that you categorically don't want X11 on your server. If that is not the case then, as I see you're using RedHat, all you need to install for emboss to compile is the XFree86-devel rpm. -------------- next part -------------- An HTML attachment was scrubbed... URL: From shibl at seqbio.com Wed Jul 31 15:55:52 2002 From: shibl at seqbio.com (Shibl Mourad) Date: Wed, 31 Jul 2002 11:55:52 -0400 Subject: Supermatcher References: <2AE73E3601DA0E428E14535564F6A9544F9397@e2knl1.nl.seedsnetwork.com> Message-ID: <01b101c238aa$c082d270$2602a8c0@SEQUENCE> RE: Instalation and D'd problem.Hi all, I am using supermatcher to align 2 sequences, and it seems that the order of the sequences affects the results dramatically (see example below). Is that normal? Shibl Note: The following examples where build by downloading AP000926.5 and AP001970.3 from entrez and then calling supermatcher with wordlen=20, all other parameters are kept as default. ######################################## # Program: supermatcher # Rundate: Wed Jul 31 11:54:34 2002 # Report_file: ap000926.supermatcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: AP000926.5 # 2: AP001970.3 # Matrix: EDNAFULL # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 57265 # Identity: 40361/57265 (70.5%) # Similarity: 40361/57265 (70.5%) # Gaps: 11627/57265 (20.3%) # Score: 133850.5 # # #======================================= ######################################## # Program: supermatcher # Rundate: Wed Jul 31 11:55:10 2002 # Report_file: ap001970.supermatcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: AP001970.3 # 2: AP000926.5 # Matrix: EDNAFULL # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 52182 # Identity: 50101/52182 (96.0%) # Similarity: 50101/52182 (96.0%) # Gaps: 1463/52182 ( 2.8%) # Score: 242805.0 # # #======================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From qingjuan at wistar.upenn.edu Wed Jul 31 20:32:21 2002 From: qingjuan at wistar.upenn.edu (Qingjuan Gu) Date: Wed, 31 Jul 2002 16:32:21 -0400 Subject: PNG format output Message-ID: <200207311632.AA140050702@wistar.upenn.edu> Hi, When I use 'dottup' and choose 'PNG' output format, there is a error message: Error: Invalid graph value 'png' oth in command line and on web site. But when I check http://bioinfo.pbi.nrc.ca:8090/EMBOSS/, the png format can work in this site. Does anybody give me some suggestions about this problem. Thanks a lot. Grace athena.wistar.upenn.edu> dottup Displays a wordmatch dotplot of two sequences Input sequence: tembl:xlrhodop Second sequence: tembl:xlrhodop Word size [10]: Display as data [N]: Graph type [x11]: png Error: Invalid graph value 'png' Devices allowed are:- postscript