From pmr at ebi.ac.uk Fri May 1 04:21:50 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 01 May 2009 09:21:50 +0100 Subject: [EMBOSS] Applications limits In-Reply-To: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> References: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Message-ID: <49FAB11E.7090502@ebi.ac.uk> Achille Zappa wrote: > Hi All ! > I'm new in the mailing list and I want to say hello to everyones > I want to use some EMBOSS apps as services in a Taverna workflow, but > they failed in some cases, I suppose when I use "too many" sequences or > alignments as inputs!! Could you tell me if there are some specific limits > and what they are?! Especially about "emma", "fproml" and "fneighbor" > services ! The applications are limited only by the resources of the machines they run on. The applications you mention are not pure EMBOSS applications. Emma is a wrapper for clustalw. fproml and fneighbor are from PHYLIP 3.6. They may have their own limits but they are large. When using Taverna and the SoapLab services you may reach a timeout limit on the services. I see Mahmut Uludag has already replied on the taverna mailing list with a fix for that. SoapLab services for Taverna use machines with large enough resources for most jobs. If you find an example where you have reached a limit, please send it to emboss-bug at emboss.open-bio.org It may be simply a large input or a long calculation - but we can try to improve the application to make it faster or to use less memory. regards, Peter Rice From achille.zappa at istge.it Tue May 5 05:04:13 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Tue, 5 May 2009 11:04:13 +0200 (CEST) Subject: [EMBOSS] Bootstrap Message-ID: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> Hi !! in my tests using emboss apps in Taverna I tried to bootstrap my alignment to obtain a phylogenetic tree. I used fseqboot to perform the bootstrapping for my proteins in this manner : alignments -> fseqboot -> fprotdist -> fneighbor but it fails and returns a message like this : ERROR 2009-05-05 10:43:02,125 Failure while executing task fneighbor uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Soapla b call returned an error : Summary: Completed: Erroneously Termination status: 139 Started: 2009-May-05 09:42:24 (BST) Ended: 2009-May-05 09:42:25 (BST) Duration: 0:00:00.411 Report: Some error messages were reported. Name: phylogeny_distance_matrix.fneighbor Job ID: phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e Program and parameters: /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/i_datafile -treetype n -outfile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/o_outfile -outtreefile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/o_outtreefiletreefile -auto --- end of parameters Exit code: 139 Standard error stream: /homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault (core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile /ebi/extser v/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7c b923b5.120e2d551e0._7f3e/i_datafile -treetype n -outfile /ebi/extserv/soaplab-wo rk/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2 d551e0._7f3e/o_outfile -outtreefile /ebi/extserv/soaplab-work/tc-soaplab-emboss4 /SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e/o_outtre efiletreefile -auto in attach there are the input file and the workflow I used. Could you tell me where is my error?! thank you regards (I'll try to send you a sample of my other apps faults later) Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it -------------- next part -------------- A non-text attachment was scrubbed... Name: M_EMBOSS_Trees_NJ_boot_b.xml Type: text/xml Size: 3809 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Muscle_Alignment.text URL: From uludag at ebi.ac.uk Tue May 5 08:05:09 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 May 2009 13:05:09 +0100 Subject: [EMBOSS] Bootstrap In-Reply-To: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> Message-ID: <1241525109.27509.203.camel@emboss2.ebi.ac.uk> Hi Achille, > /homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault > (core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile It looks like fneighbor program is not happy with the input data provided. Unfortunately a bug in EMBOSS version 4.1 doesn't let error messages printed but the program crashes. However if I run the same input data with latest EMBOSS (6.0.1) I get the following error messages. Error: Distance file i_datafile: Row ' 3.527346' has 9 values Error: Distance file i_datafile: Row ' 5.470720' has 8 values Error: Distance file i_datafile: Row ' 4.804096' has 8 values ............ Error: Distance file i_datafile: Row 'ACC97187.1' has 11 values in square format Error: Distance file i_datafile: Row ' 0.000000' has 8 values Error: Distance file i_datafile: Row 'NP_082292.' has 0 values in square format Error: Distance file i_datafile: Row ' 4.733737' has 8 values in square format ............ Error: Distance file i_datafile: Row ' 4.151302' has 8 values Error: Distances file found 2 rows, expected 15 Error: Unable to read distances file 'i_datafile' It would be advisable to use EBI main Soaplab services which includes EMBOSS-6.0.1 applications, instead of Soaplab services for EMBOSS 4.1 which is selected by default in Taverna-1.7.1. You can make this change by editing taverna.defaultsoaplab entry in your taverna conf/mygrid.properties file as follows. taverna.defaultsoaplab = http://www.ebi.ac.uk/soaplab/services After this change you need to restart taverna and delete and redefine your Soaplab Processors (if it is too much work then you can at least redefine fneighboor Processor as it is crashing with EMBOSS-4.1 and use main Soaplab services for Processors you will define in future). I cc this message to Alan and Stuart from Taverna team for information. They were planning to change default Soaplab endpoint to main EBI Soaplab services in the next release of Taverna-1.7 series. Regards, Mahmut From achille.zappa at istge.it Wed May 6 03:30:04 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Wed, 6 May 2009 09:30:04 +0200 (CEST) Subject: [EMBOSS] Bootstrap In-Reply-To: <1241525109.27509.203.camel@emboss2.ebi.ac.uk> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> <1241525109.27509.203.camel@emboss2.ebi.ac.uk> Message-ID: <1444.10.2.0.90.1241595004.squirrel@webmail.istge.it> > Hi !! > taverna.defaultsoaplab = http://www.ebi.ac.uk/soaplab/services > > After this change you need to restart taverna and delete and redefine > your Soaplab Processors (if it is too much work then you can at least > redefine fneighboor Processor as it is crashing with EMBOSS-4.1 and use > main Soaplab services for Processors you will define in future). > > I cc this message to Alan and Stuart from Taverna team for information. > They were planning to change default Soaplab endpoint to main EBI > Soaplab services in the next release of Taverna-1.7 series. > > Regards, > Mahmut > Thank you for your help I loaded the new soaplab services and now I'll try them. They are a little bit different , in ebi style with poll! and external params, but surely more reliable ok. regards Achille Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From michael.watson at bbsrc.ac.uk Mon May 11 10:12:20 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Mon, 11 May 2009 15:12:20 +0100 Subject: [EMBOSS] Problems installing EMBASSY: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory Message-ID: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> Hi I am running RHEL 4 and just installed EMBOSS 6.0.1 in /usr/local/EMBOSS I downloaded ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.67.tar.gz and tried to install that. I used ./configure --prefix=/usr/local/EMBOSS and then tried make. The results are below. Any help? What is plplot.h? Thanks Mick -bash-3.00# make Making all in src make[1]: Entering directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\" -DVERSION=\"3.67\" -DSTDC_HEADER S=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_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_ FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I../include -I/usr/local/EMBOSS/incl ude -I/usr/local/EMBOSS/include/eplplot -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/include//include -DNO_AUTH -O2 -MT clique.o -MD -MP -MF .deps/clique.Tpo -c -o clique.o clique.c In file included from /usr/local/include/emboss.h:5, from ../include/phylip.h:30, from clique.c:1: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory In file included from /usr/local/include/emboss.h:5, from ../include/phylip.h:30, from clique.c:1: /usr/local/include/ajgraph.h:81: error: syntax error before "xx0" /usr/local/include/ajgraph.h:82: error: syntax error before "xx0" /usr/local/include/ajgraph.h:84: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:115: error: syntax error before "xx0" /usr/local/include/ajgraph.h:116: error: syntax error before "xx0" /usr/local/include/ajgraph.h:117: error: syntax error before '*' token /usr/local/include/ajgraph.h:135: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:146: error: syntax error before "xx1" /usr/local/include/ajgraph.h:147: error: syntax error before '*' token /usr/local/include/ajgraph.h:162: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:169: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:170: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:172: error: syntax error before "xx0" /usr/local/include/ajgraph.h:173: error: syntax error before "xx0" /usr/local/include/ajgraph.h:189: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:191: error: syntax error before "xx1" /usr/local/include/ajgraph.h:192: error: syntax error before "xx1" /usr/local/include/ajgraph.h:193: error: syntax error before "xx1" /usr/local/include/ajgraph.h:194: error: syntax error before "xx1" /usr/local/include/ajgraph.h:196: error: syntax error before "xx1" /usr/local/include/ajgraph.h:198: error: syntax error before "xx1" /usr/local/include/ajgraph.h:200: error: syntax error before "xx1" /usr/local/include/ajgraph.h:203: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:283: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:285: error: syntax error before '*' token /usr/local/include/ajgraph.h:285: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:287: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:291: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:294: error: syntax error before "ajGraphTextLength" /usr/local/include/ajgraph.h:294: error: syntax error before "xx1" /usr/local/include/ajgraph.h:296: error: syntax error before "ajGraphTextHeight" /usr/local/include/ajgraph.h:296: error: syntax error before "xx1" /usr/local/include/ajgraph.h:297: error: syntax error before "ajGraphDistPts" /usr/local/include/ajgraph.h:297: error: syntax error before "xx1" /usr/local/include/ajgraph.h:298: error: syntax error before "ajGraphFitTextOnLine" /usr/local/include/ajgraph.h:298: error: syntax error before "xx1" /usr/local/include/ajgraph.h:302: error: syntax error before "xcentre" make[1]: *** [clique.o] Error 1 make[1]: Leaving directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' make: *** [all-recursive] Error 1 Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately. Unauthorised use, disclosure, copying or alteration of this message is forbidden & may be unlawful. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute. This email, and associated attachments, has been checked locally for viruses but we can accept no responsibility once it has left our systems. Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes. The Institute for Animal Health is a company limited by guarantee, registered in England no. 559784. The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From ajb at ebi.ac.uk Mon May 11 11:21:20 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 11 May 2009 16:21:20 +0100 (BST) Subject: [EMBOSS] Problems installing EMBASSY: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> References: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> Message-ID: <53068.86.26.12.63.1242055280.squirrel@webmail.ebi.ac.uk> Hi Mick, It looks, from the following: > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory that you may have an old installation of EMBOSS under /usr/local (or bits of an old installation) i.e. it is looking in /usr/local/include rather than /usr/local/EMBOSS/include. The gcc compiler will usually look under /usr/include and /usr/local/include automatically and preferentially, so anything there will tend to override anything in /usr/local/EMBOSS/include. It is also unusual to see "-I/usr/include//include" there (perhaps a rogue CFLAGS environment variable somewhere or some manual editing of the makefiles), but the definition is meaningless and harmless (unless someone has been installing software under /usr/include). plplot.h is provided as part of the EMBOSS distribution (usually in /fu/bar/emboss/include/eplplot) and contains definitions for the graphics system. HTH Alan > Hi > > > > I am running RHEL 4 and just installed EMBOSS 6.0.1 in /usr/local/EMBOSS > > > > I downloaded ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.67.tar.gz > and tried to install that. > > > > I used ./configure --prefix=/usr/local/EMBOSS and then tried make. The > results are below. > > > > Any help? What is plplot.h? > > > > Thanks > > Mick > > > > -bash-3.00# make > > Making all in src > > make[1]: Entering directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\" > -DVERSION=\"3.67\" -DSTDC_HEADER > > S=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_STDINT_H=1 -DHAVE_UNISTD_H=1 > > -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 > -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 > -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_ > > FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 > -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. > -I../include -I/usr/local/EMBOSS/incl > > ude -I/usr/local/EMBOSS/include/eplplot -DAJ_LinuxLF > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE > -DLENDIAN -I/usr/include//include -DNO_AUTH -O2 -MT > > clique.o -MD -MP -MF .deps/clique.Tpo -c -o clique.o clique.c > > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory > > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:81: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:82: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:84: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:115: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:116: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:117: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:135: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:146: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:147: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:162: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:169: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:170: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:172: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:173: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:189: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:191: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:192: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:193: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:194: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:196: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:198: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:200: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:203: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:283: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:285: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:285: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:287: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:291: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:294: error: syntax error before > "ajGraphTextLength" > > /usr/local/include/ajgraph.h:294: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:296: error: syntax error before > "ajGraphTextHeight" > > /usr/local/include/ajgraph.h:296: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:297: error: syntax error before > "ajGraphDistPts" > > /usr/local/include/ajgraph.h:297: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:298: error: syntax error before > "ajGraphFitTextOnLine" > > /usr/local/include/ajgraph.h:298: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:302: error: syntax error before "xcentre" > > make[1]: *** [clique.o] Error 1 > > make[1]: Leaving directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' > > make: *** [all-recursive] Error 1 > > > > Head of Bioinformatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > > > Please consider the environment and don't print this e-mail unless you > really need to. > > The information contained in this message may be confidential or legally > privileged and is intended solely for the addressee. If you have > received this message in error please delete it & notify the originator > immediately. Unauthorised use, disclosure, copying or alteration of > this message is forbidden & may be unlawful. The contents of this > e-mail are the views of the sender and do not necessarily represent the > views of the Institute. This email, and associated attachments, has > been checked locally for viruses but we can accept no responsibility > once it has left our systems. Communications on Institute computers are > monitored to secure the effective operation of the systems and for other > lawful purposes. > > > > The Institute for Animal Health is a company limited by guarantee, > registered in England no. 559784. > > The Institute is also a registered charity, Charity Commissioners > Reference No. 228824 > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From uludag at ebi.ac.uk Mon May 11 11:36:12 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Mon, 11 May 2009 16:36:12 +0100 Subject: [EMBOSS] [Taverna-users] Bootstrap In-Reply-To: <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> <1241626362.1002.107.camel@emboss2.ebi.ac.uk><4A042DB0.9060403@ebi.ac.uk> <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> Message-ID: <1242056172.30340.192.camel@emboss2.ebi.ac.uk> Hi Achille, > - the fneighbor app fails everytime with errors like this : > Error: Distances file found 0 rows, expected 15 This problem looks like have been fixed in CVS version of EMBOSS, as i get reasonable output when i run CVS version of fneighbor with your input file. This suggests current patches don't include the fixes I thought they have. It is my fault that i didn't double check it before returning you. > I don't understand the "Standard error stream" explanation! about datafile > and the "-auto" param. "-auto" is an emboss parameter which means EMBOSS should try runing an application without asking further questions but using the inputs/parameters available on the command line. We will consider removing it from Soaplab job reports. "Standard error stream" is a term used by Soaplab meaning "error output of the job", it looks like we can improve its wording. > Instead If I use, for exsample, a 48 sequences alignment input I have a > java heap space error (is it my computer fault?). This is most probably related to memory used by your Taverna Java process. I tested your 48 sequence alignment with all 3 workflows attached, i didn't get any memory errors but i use a quite generous -Xmx setting in my runme.sh file. You may try increasing the default -Xmx setting in your taverna runme.sh file. Alternatively, as far as i know memory used grows each time i run a new workflow in taverna, you may try closing existing workflow run tabs before running a new workflow. > -the timeout limit for the jobs is 60 minutes!? , it is a restriction of > EBI that is impossible to avoid I suppose! this was a good enough timeout limit previously, i think we can increase it, let me discuss this with relevant people, if i execute the same fproml job outside LSF it takes about 80 minutes which suggests a 2 hour limit should allow your fproml jobs completed. > for example a fproml job with 48 seq align is more than 60 minutes long I > think because after 1 hour it returns a completed job message with empty > output. This is a bug in Soaplab (introduced by me), it should report the status terminated, rather than completed successfully. Regards, Mahmut From maoj at helix.nih.gov Tue May 12 10:11:20 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Tue, 12 May 2009 10:11:20 -0400 Subject: [EMBOSS] Error in edialign Message-ID: <4A098388.6070900@helix.nih.gov> Hi, When I run emboss-6.0.1 'edialign' program on command line, I saw this error: Error: File /usr/local/EMBOSS-6.0.1/share/EMBOSS/acd/edialign.acd line 124: (outseq) Attribute 'aligned' unknown The edialign.acd file was attached. Thank you. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: edialign.acd URL: From ajb at ebi.ac.uk Tue May 12 11:22:34 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 12 May 2009 16:22:34 +0100 (BST) Subject: [EMBOSS] Error in edialign In-Reply-To: <4A098388.6070900@helix.nih.gov> References: <4A098388.6070900@helix.nih.gov> Message-ID: <42293.86.26.12.63.1242141754.squirrel@webmail.ebi.ac.uk> Hi Jean, That problem was addressed by a recent patch put on the ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ Let us know if it doesn't fix it for you. HTH Alan > Hi, > > When I run emboss-6.0.1 'edialign' program on command line, I saw this > error: > Error: File /usr/local/EMBOSS-6.0.1/share/EMBOSS/acd/edialign.acd line > 124: (outseq) Attribute 'aligned' unknown > > The edialign.acd file was attached. > > Thank you. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jerome at ibt.unam.mx Wed May 13 18:34:26 2009 From: jerome at ibt.unam.mx (Jerome) Date: Wed, 13 May 2009 17:34:26 -0500 Subject: [EMBOSS] fdnadist and fneighbor issue Message-ID: <4A0B4AF2.4080006@ibt.unam.mx> Dear all I'm using emboss 5.0 version, and come out of some problem. I've got a alignment of 15 dna sequence, generated by clustalw (emma). Thsi file is in fatsa format. I want to calculate the distance between all of this using fdnadist: $fdnadist -sequence globin-align.fasta -method f -outfile globin.fnadist All run without problem, and my output file is like this: 15 CHIHBA1 0.000000 0.010022 0.264744 0.167372 0.315764 0.319542 0.394008 0.397425 0.500520 0.498700 0.696916 1.352558 1.223696 1.327388 1.223196 CHIHBB1 0.010022 0.000000 0.226115 0.171012 0.318000 0.321806 0.403662 0.403176 0.510729 0.508896 0.696097 1.333125 1.241254 ../.. This file format seems to generate a issu with fneighbor, as it complains about 0 rows found in place of 15: $ fneighbor -datafile globin.fnadist -outfile globin.fneighbor Phylogenies from distance matrix by N-J or UPGMA method Error: Distances file found 0 rows, expected 15 Error: Unable to read distances file 'globin.fnadist' Died: fneighbor terminated: Bad value for '-datafile' and no prompt This problem disapeared if i format the distance file in one line for each sequence. As i do all of this command as default, maybe i forgot a option in the fdnadist ? This command is inside a flow of cemboss commands, so it's complicated for me to edit by hand each distance file to be "correct" for fneighbor.. Someone can explain me where i'm wrong? Regards -- -- J?r?me Moi j'aime bien quand M. Bl?durt raconte ses histoires de guerre, une fois il m'a expliqu? comment il a captur?, tout seul, un sous-marin pleins d'ennemis. (Histoires in?dites du Petit Nicolas, Goscinny & Semp?) From michael.watson at bbsrc.ac.uk Thu May 14 07:47:09 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 14 May 2009 12:47:09 +0100 Subject: [EMBOSS] fdnaml prompts for (optional) Phylip tree from command line Message-ID: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> Hi Running Emboss 6.01 with PHYLIPNEW installed (3.67) When I run fdnaml from the command line it always prompts for a philip tree, which is supposedly optional. I know from the docs I should be able to turn this off using -options but I can't find out what I can say to -options to make it stop. fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree -options=F Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree -options=0 Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): Please forgive me if I'm doing something silly.... Mick Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately. Unauthorised use, disclosure, copying or alteration of this message is forbidden & may be unlawful. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute. This email, and associated attachments, has been checked locally for viruses but we can accept no responsibility once it has left our systems. Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes. The Institute for Animal Health is a company limited by guarantee, registered in England no. 559784. The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From pmr at ebi.ac.uk Thu May 14 08:35:51 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 14 May 2009 13:35:51 +0100 Subject: [EMBOSS] fdnaml prompts for (optional) Phylip tree from command line In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> References: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> Message-ID: <4A0C1027.3040205@ebi.ac.uk> michael watson (IAH-C) wrote: > When I run fdnaml from the command line it always prompts for a philip > tree, which is supposedly optional. You can just hit return - if you do not give a tree file it will be ignored. You can also use -auto to accept the defaults for any other options. You can also put -nointreefile or -intreefile "" or -intreefile="" on the command line. "(optional)" in the prompt is just for information, there is nothing automatic about it. Perhaps we can find a standard way to say that an empty value is accepted (in the ACD file it has nullok set true). Hope that helps, Peter From pmr at ebi.ac.uk Fri May 15 06:15:26 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 15 May 2009 11:15:26 +0100 Subject: [EMBOSS] fdnadist and fneighbor issue In-Reply-To: <4A0B4AF2.4080006@ibt.unam.mx> References: <4A0B4AF2.4080006@ibt.unam.mx> Message-ID: <4A0D40BE.3010607@ebi.ac.uk> Dear Jerome, > I'm using emboss 5.0 version, and come out of some problem. > I've got a alignment of 15 dna sequence, generated by clustalw (emma). > > This file format seems to generate a issu with fneighbor, as it > complains about 0 rows found in place of 15: > > This problem disapeared if i format the distance file in one line for > each sequence. As i do all of this command as default, maybe i forgot a > option in the fdnadist ? This command is inside a flow of cemboss > commands, so it's complicated for me to edit by hand each distance file > to be "correct" for fneighbor.. There is a known problem with distance file formats. For EMBOSS 6.0.1 there is a patch available to correct the ajphylo.c source file. I am working through updating to phylip 3.68 and there are some new format issues with distance matrix files. They will be included in the July release. If you need a fix for EMBOSS 5.0 then we can try sending you a corrected 5.0 ajphylo.c source file. Hope this helps, Peter From achille.zappa at istge.it Mon May 11 09:04:26 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Mon, 11 May 2009 15:04:26 +0200 (CEST) Subject: [EMBOSS] Bootstrap In-Reply-To: <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it><1241626362.1002.107.camel@emboss2.ebi.ac.uk><4A042DB0.9060403@ebi.ac.uk> <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> Message-ID: <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> > Hi Hamish, >> EMBOSS 6.0.1 install updated with current patches. > Thanks. > Achille, I would appreciate it if you can update your workflow to Soaplab > EMBOSS-6 services and check whether you now get correct results. Please > let us know if you still get erroneous results. > Regards, > Mahmut HI I made some tests with EMBOSS-6 apps in Taverna 1.7.1, but i had bad result, problably my faults because I haven't still exactly understand how to use them. I'll try to explain my doubts, sorry if it could be a little confused : primarly my objective is to create phylogenetic trees of protein sequences, so i use FASTA sequences for -> multiple alignments tolls to -> create phylo trees with distance matrix (nj and/or UPGMA) or Maximum Likelihood tools. For this I implemented in my workflow also a part like that in the attach files : - are the construction of the workflow, and connection links right? - the fneighbor app fails everytime with errors like this : " Soaplab call returned an error : Summary: Completed: Erroneously Report: Some error messages were reported. Name: phylogeny_distance_matrix.fneighbor Job ID: [phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 Program and parameters: /ebi/extserv/bin/EMBOSS-6.0.1/bin/fneighbor -datafile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/i_datafile -outfile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/o_outfile -outtreefile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 /o_outtreefiletreefile -auto --- end of parameters Exit code: 1 Standard error stream: Error: Distances file found 0 rows, expected 15 Error: Unable to read distances file '/ebi/extserv/soaplab- work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 /i_datafile' Died: fneighbor terminated: Bad value for '-datafile' with -auto defined
SoaplabTask.execute(..) : line 146 <SoaplabTask.java>
ProcessorTask.runAndGenerateTemplates(..) : line 576 <ProcessorTask.java>
ProcessorTask.doInvocationWithRetryLogic(..) : line 517 <ProcessorTask.java>
ProcessorTask.invokeOnce(..) : line 436 <ProcessorTask.java>
ProcessorTask.invokeWithoutIteration(..) : line 642 <ProcessorTask.java>
ProcessorTask.invoke(..) : line 353 <ProcessorTask.java>
ProcessorTask.handleRun(..) : line 280 <ProcessorTask.java>
NewState$1.run(..) : line 67 <NewState.java>
] " I don't understand the "Standard error stream" explanation! about datafile and the "-auto" param. In attach also some input samples. Instead If I use, for exsample, a 48 sequences alignment input I have a java heap space error (is it my computer fault?). -the timeout limit for the jobs is 60 minutes!? , it is a restriction of EBI that is impossible to avoid I suppose! for example a fproml job with 48 seq align is more than 60 minutes long I think because after 1 hour it returns a completed job message with empty output. I apologize if all this stuff is only a my fault becuase of my ignorance about these processes but I will appreciate your help and advices. Thank you all for your time and disponibility BEST REGARDS CHEERS Achille P.S. Do you have some advices about the best tools for a phylogenetic tree research, about different alignment apps (ClustalW, Muscle, T-coffee, ....) different distance algorythm (NJ, UPGMA, MAX Likelihood, ....), tree constuction, computational optimization ... THANKS -- Achille Zappa -Bioinformatics National Cancer Research Institute (IST) Largo Benzi 10 16132 Genova - ITALY Tel. 010 5737288 -IEIIT - Sezione di Genova National Research Council (CNR) via De Marini, 6 16149 Genova - ITALY Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it -------------- next part -------------- A non-text attachment was scrubbed... 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Name: Muscle_Alignment.text URL: From karenryder1 at yahoo.com Tue May 19 22:26:02 2009 From: karenryder1 at yahoo.com (Karen Ryder) Date: Tue, 19 May 2009 19:26:02 -0700 (PDT) Subject: [EMBOSS] Program does not show up in menu Message-ID: <576741.76968.qm@web111615.mail.gq1.yahoo.com> I downloaded emboss from the synaptic package manager in Ubuntu (Jaunty) and it doesn't show up in the menu. I did a search for "emboss" in the filesystem, and found that some of the folders are in usr/share and in etc/ but I couldn't find the launch file. I have uninstall/reinstall from the package manager and rebooted my laptop but still nothing changes. What do I do? From charles-listes-emboss at plessy.org Wed May 20 00:16:38 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 20 May 2009 13:16:38 +0900 Subject: [EMBOSS] Program does not show up in menu In-Reply-To: <576741.76968.qm@web111615.mail.gq1.yahoo.com> References: <576741.76968.qm@web111615.mail.gq1.yahoo.com> Message-ID: <20090520041637.GA14310@kunpuu.plessy.org> Le Tue, May 19, 2009 at 07:26:02PM -0700, Karen Ryder a ?crit : > I downloaded emboss from the synaptic package manager in Ubuntu (Jaunty) and > it doesn't show up in the menu. I did a search for "emboss" in the > filesystem, and found that some of the folders are in usr/share and in etc/ > but I couldn't find the launch file. I have uninstall/reinstall from the > package manager and rebooted my laptop but still nothing changes. What do I > do? Dear Karen, EMBOSS is a suite of command line programs, so they will not be seen from the menu of your graphical session. If you look for an interface packaged in Ubuntu, then I would like to suggets ?EMBOSS Explorer? (package emboss-explorer). Alternatively, you can try Jemboss, but this package is still very untested (feedback welcome!) and was never part of a stable Debian release (the EMBOSS packages on Ubuntu are originally made for Debian). If there are other interfaces that you are used to and would like to suggest for packaging, please do not hesitate to let me know. I was considering EMBOSS-kaptain, but I am affraid that both projects (EMBOSS-kaptain and Kaptain itself) are inactive for a long time, and I do not know how well they would work with KDE?4? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From Veronique.Martin at jouy.inra.fr Mon May 25 10:22:46 2009 From: Veronique.Martin at jouy.inra.fr (Veronique.Martin at jouy.inra.fr) Date: Mon, 25 May 2009 16:22:46 +0200 (CEST) Subject: [EMBOSS] whichdb error Message-ID: Hi all, I have this error with whichdb command: ----------- whichdb -showall Search all sequence databases for an entry and retrieve it ID or Accession number: L07770 Output file [stdout]: # Trying 'gb_rod:l07770' # Failed 'gb_rod:l07770' # Trying 'gb_pln:l07770' # Failed 'gb_pln:l07770' # Trying 'gp_syn:l07770' # Failed 'gp_syn:l07770' # Trying 'gb_pri:l07770' # Failed 'gb_pri:l07770' # Trying 'genbankwgs:l07770' # Failed 'genbankwgs:l07770' # Trying 'nr80:l07770' # Failed 'nr80:l07770' # Trying 'PRINTS:l07770' Warning: Cannot open division file '' for database 'PRINTS' Warning: seqCdQry failed # Failed 'PRINTS:l07770' # Trying 'opsdw:l07770' # Failed 'opsdw:l07770' # Trying 'emblwgs_hum:l07770' EMBOSS An error in ajindex.c at line 2429: GetKeys: No keys in node ------------ However, it's ok for this ID, because for example, infoseq or other commands (seqret...) runs correctly, as you can see bellow: ------------- infoseq genbank:l07770 Display basic information about sequences USA Database Name Accession Type Length %GC Description genbank-id:XELRHODOP genbank XELRHODOP L07770 N 1684 45.72 Xenopus laevis rhodopsin mRNA, complete cds. ------------- I run emboss 6.0.1 Any help? Thanks Veronique ------------------------------------------------- V?ronique MARTIN INRA - Unit? Math?matique, Informatique et G?nome 78352 Jouy-en Josas cedex tel.: 01 34 65 29 74 ------------------------------------------------- From noreply at netlogmail.com Tue May 26 00:44:14 2009 From: noreply at netlogmail.com (Duleep Samuel) Date: Tue, 26 May 2009 00:44:14 -0400 Subject: [EMBOSS] Visit my Netlog profile Message-ID: <200905260444.n4Q4iEWt014703@portal.open-bio.org> Hey, I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile. Take a look: http://en.netlog.com/go/mailurl/type=invite_1&mailid=319267176&id=1&url=-L2dvL3JlZ2lzdGVyL2lkPTEwODYwNTk3NzImaT10OTE_ Greetings, Duleep ---------------------------------------------------------------- Don't you wish to receive these e-mails? No longer wish to receive Netlog e-mails? http://en.netlog.com/go/mailurl/type=invite_1&mailid=319267176&id=2&url=-L2dvL25vbWFpbHMvaW52aXRlL2VtYWlsPS1aVzFpYjNOelFHeHBjM1J6TG05d1pXNHRZbWx2TG05eVp3X18mY29kZT0xMjEwMTAxMyZpZD0xMDg2MDU5NzcyJmk9dDky From pmr at ebi.ac.uk Tue May 26 16:07:13 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 26 May 2009 21:07:13 +0100 Subject: [EMBOSS] whichdb error In-Reply-To: References: Message-ID: <4A1C4BF1.2050507@ebi.ac.uk> Veronique.Martin at jouy.inra.fr wrote: > I have this error with whichdb command: Whichdb will search for L07770 by ID and by accession in all the databases you have defined. The outputn will show a list of all the databases it tests, which will be defined in your emboss.defaults file and perhaps in your personal ~/.embossrc file > ----------- > whichdb -showall > Search all sequence databases for an entry and retrieve it > ID or Accession number: L07770 > Output file [stdout]: > # Trying 'gb_rod:l07770' > # Failed 'gb_rod:l07770' > # Trying 'gb_pln:l07770' > # Failed 'gb_pln:l07770' > # Trying 'gp_syn:l07770' > # Failed 'gp_syn:l07770' > # Trying 'gb_pri:l07770' > # Failed 'gb_pri:l07770' > # Trying 'genbankwgs:l07770' > # Failed 'genbankwgs:l07770' > # Trying 'nr80:l07770' > # Failed 'nr80:l07770' > # Trying 'PRINTS:l07770' > Warning: Cannot open division file '' for database 'PRINTS' > Warning: seqCdQry failed This suggests you have PRINTS defined as a sequence database. Prints is a pattern database and does not need to be defined in emboss.defaults of ~/.embossrc > # Failed 'PRINTS:l07770' > # Trying 'opsdw:l07770' > # Failed 'opsdw:l07770' > # Trying 'emblwgs_hum:l07770' > > EMBOSS An error in ajindex.c at line 2429: > GetKeys: No keys in node > ------------ and this suggests a problem with the indexing of your emblwgs_hum database. You need to check the status of this database and correct it. Meanwhile, perhaps we can persuade whichdb to continue checking the remaining databases. You failed to find L07770 because it stopped at this point. > However, it's ok for this ID, because for example, > infoseq or other commands (seqret...) runs correctly, as you can see > bellow: > ------------- > infoseq genbank:l07770 > Display basic information about sequences > USA Database Name Accession Type > Length %GC Description > genbank-id:XELRHODOP genbank XELRHODOP L07770 N > 1684 45.72 Xenopus laevis rhodopsin mRNA, complete cds. So whichdb will find the entry when it reaches genbank and searched by accession. I hope this helps. Let us know (mail to emboss-bug at emboss.open-bio.org) if you need help in correcting your databases. regards, Peter Rice From maoj at helix.nih.gov Wed May 27 08:40:53 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 27 May 2009 08:40:53 -0400 Subject: [EMBOSS] Alternative splicing applications in EMBOSS? Message-ID: <4A1D34D5.1000503@helix.nih.gov> Hi, I have tried to search EMBOSS to see if it has applications for alternative splicing analysis of a gene of interest but no luck. Just want to ask here in case I missed any. Thank you. Jean From pmr at ebi.ac.uk Wed May 27 09:06:52 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 27 May 2009 14:06:52 +0100 Subject: [EMBOSS] Alternative splicing applications in EMBOSS? In-Reply-To: <4A1D34D5.1000503@helix.nih.gov> References: <4A1D34D5.1000503@helix.nih.gov> Message-ID: <4A1D3AEC.2010206@ebi.ac.uk> Jean Mao wrote: > Hi, > > I have tried to search EMBOSS to see if it has applications for > alternative splicing analysis of a gene of interest but no luck. Just > want to ask here in case I missed any. Thank you. We are very interested in suggestions for new applications. What alternative splicing analysis do you need? regards, Peter From pmr at ebi.ac.uk Fri May 1 08:21:50 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 01 May 2009 09:21:50 +0100 Subject: [EMBOSS] Applications limits In-Reply-To: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> References: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Message-ID: <49FAB11E.7090502@ebi.ac.uk> Achille Zappa wrote: > Hi All ! > I'm new in the mailing list and I want to say hello to everyones > I want to use some EMBOSS apps as services in a Taverna workflow, but > they failed in some cases, I suppose when I use "too many" sequences or > alignments as inputs!! Could you tell me if there are some specific limits > and what they are?! Especially about "emma", "fproml" and "fneighbor" > services ! The applications are limited only by the resources of the machines they run on. The applications you mention are not pure EMBOSS applications. Emma is a wrapper for clustalw. fproml and fneighbor are from PHYLIP 3.6. They may have their own limits but they are large. When using Taverna and the SoapLab services you may reach a timeout limit on the services. I see Mahmut Uludag has already replied on the taverna mailing list with a fix for that. SoapLab services for Taverna use machines with large enough resources for most jobs. If you find an example where you have reached a limit, please send it to emboss-bug at emboss.open-bio.org It may be simply a large input or a long calculation - but we can try to improve the application to make it faster or to use less memory. regards, Peter Rice From achille.zappa at istge.it Tue May 5 09:04:13 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Tue, 5 May 2009 11:04:13 +0200 (CEST) Subject: [EMBOSS] Bootstrap Message-ID: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> Hi !! in my tests using emboss apps in Taverna I tried to bootstrap my alignment to obtain a phylogenetic tree. I used fseqboot to perform the bootstrapping for my proteins in this manner : alignments -> fseqboot -> fprotdist -> fneighbor but it fails and returns a message like this : ERROR 2009-05-05 10:43:02,125 Failure while executing task fneighbor uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Soapla b call returned an error : Summary: Completed: Erroneously Termination status: 139 Started: 2009-May-05 09:42:24 (BST) Ended: 2009-May-05 09:42:25 (BST) Duration: 0:00:00.411 Report: Some error messages were reported. Name: phylogeny_distance_matrix.fneighbor Job ID: phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e Program and parameters: /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/i_datafile -treetype n -outfile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/o_outfile -outtreefile /ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f neighbor_7cb923b5.120e2d551e0._7f3e/o_outtreefiletreefile -auto --- end of parameters Exit code: 139 Standard error stream: /homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault (core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile /ebi/extser v/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7c b923b5.120e2d551e0._7f3e/i_datafile -treetype n -outfile /ebi/extserv/soaplab-wo rk/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2 d551e0._7f3e/o_outfile -outtreefile /ebi/extserv/soaplab-work/tc-soaplab-emboss4 /SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e/o_outtre efiletreefile -auto in attach there are the input file and the workflow I used. Could you tell me where is my error?! thank you regards (I'll try to send you a sample of my other apps faults later) Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it -------------- next part -------------- A non-text attachment was scrubbed... Name: M_EMBOSS_Trees_NJ_boot_b.xml Type: text/xml Size: 3809 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Muscle_Alignment.text URL: From uludag at ebi.ac.uk Tue May 5 12:05:09 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 May 2009 13:05:09 +0100 Subject: [EMBOSS] Bootstrap In-Reply-To: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> Message-ID: <1241525109.27509.203.camel@emboss2.ebi.ac.uk> Hi Achille, > /homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault > (core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile It looks like fneighbor program is not happy with the input data provided. Unfortunately a bug in EMBOSS version 4.1 doesn't let error messages printed but the program crashes. However if I run the same input data with latest EMBOSS (6.0.1) I get the following error messages. Error: Distance file i_datafile: Row ' 3.527346' has 9 values Error: Distance file i_datafile: Row ' 5.470720' has 8 values Error: Distance file i_datafile: Row ' 4.804096' has 8 values ............ Error: Distance file i_datafile: Row 'ACC97187.1' has 11 values in square format Error: Distance file i_datafile: Row ' 0.000000' has 8 values Error: Distance file i_datafile: Row 'NP_082292.' has 0 values in square format Error: Distance file i_datafile: Row ' 4.733737' has 8 values in square format ............ Error: Distance file i_datafile: Row ' 4.151302' has 8 values Error: Distances file found 2 rows, expected 15 Error: Unable to read distances file 'i_datafile' It would be advisable to use EBI main Soaplab services which includes EMBOSS-6.0.1 applications, instead of Soaplab services for EMBOSS 4.1 which is selected by default in Taverna-1.7.1. You can make this change by editing taverna.defaultsoaplab entry in your taverna conf/mygrid.properties file as follows. taverna.defaultsoaplab = http://www.ebi.ac.uk/soaplab/services After this change you need to restart taverna and delete and redefine your Soaplab Processors (if it is too much work then you can at least redefine fneighboor Processor as it is crashing with EMBOSS-4.1 and use main Soaplab services for Processors you will define in future). I cc this message to Alan and Stuart from Taverna team for information. They were planning to change default Soaplab endpoint to main EBI Soaplab services in the next release of Taverna-1.7 series. Regards, Mahmut From achille.zappa at istge.it Wed May 6 07:30:04 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Wed, 6 May 2009 09:30:04 +0200 (CEST) Subject: [EMBOSS] Bootstrap In-Reply-To: <1241525109.27509.203.camel@emboss2.ebi.ac.uk> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> <1241525109.27509.203.camel@emboss2.ebi.ac.uk> Message-ID: <1444.10.2.0.90.1241595004.squirrel@webmail.istge.it> > Hi !! > taverna.defaultsoaplab = http://www.ebi.ac.uk/soaplab/services > > After this change you need to restart taverna and delete and redefine > your Soaplab Processors (if it is too much work then you can at least > redefine fneighboor Processor as it is crashing with EMBOSS-4.1 and use > main Soaplab services for Processors you will define in future). > > I cc this message to Alan and Stuart from Taverna team for information. > They were planning to change default Soaplab endpoint to main EBI > Soaplab services in the next release of Taverna-1.7 series. > > Regards, > Mahmut > Thank you for your help I loaded the new soaplab services and now I'll try them. They are a little bit different , in ebi style with poll! and external params, but surely more reliable ok. regards Achille Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From michael.watson at bbsrc.ac.uk Mon May 11 14:12:20 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Mon, 11 May 2009 15:12:20 +0100 Subject: [EMBOSS] Problems installing EMBASSY: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory Message-ID: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> Hi I am running RHEL 4 and just installed EMBOSS 6.0.1 in /usr/local/EMBOSS I downloaded ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.67.tar.gz and tried to install that. I used ./configure --prefix=/usr/local/EMBOSS and then tried make. The results are below. Any help? What is plplot.h? Thanks Mick -bash-3.00# make Making all in src make[1]: Entering directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\" -DVERSION=\"3.67\" -DSTDC_HEADER S=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_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_ FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I../include -I/usr/local/EMBOSS/incl ude -I/usr/local/EMBOSS/include/eplplot -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -I/usr/include//include -DNO_AUTH -O2 -MT clique.o -MD -MP -MF .deps/clique.Tpo -c -o clique.o clique.c In file included from /usr/local/include/emboss.h:5, from ../include/phylip.h:30, from clique.c:1: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory In file included from /usr/local/include/emboss.h:5, from ../include/phylip.h:30, from clique.c:1: /usr/local/include/ajgraph.h:81: error: syntax error before "xx0" /usr/local/include/ajgraph.h:82: error: syntax error before "xx0" /usr/local/include/ajgraph.h:84: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:115: error: syntax error before "xx0" /usr/local/include/ajgraph.h:116: error: syntax error before "xx0" /usr/local/include/ajgraph.h:117: error: syntax error before '*' token /usr/local/include/ajgraph.h:135: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:146: error: syntax error before "xx1" /usr/local/include/ajgraph.h:147: error: syntax error before '*' token /usr/local/include/ajgraph.h:162: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:169: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:170: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:172: error: syntax error before "xx0" /usr/local/include/ajgraph.h:173: error: syntax error before "xx0" /usr/local/include/ajgraph.h:189: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:191: error: syntax error before "xx1" /usr/local/include/ajgraph.h:192: error: syntax error before "xx1" /usr/local/include/ajgraph.h:193: error: syntax error before "xx1" /usr/local/include/ajgraph.h:194: error: syntax error before "xx1" /usr/local/include/ajgraph.h:196: error: syntax error before "xx1" /usr/local/include/ajgraph.h:198: error: syntax error before "xx1" /usr/local/include/ajgraph.h:200: error: syntax error before "xx1" /usr/local/include/ajgraph.h:203: error: syntax error before "PLFLT" /usr/local/include/ajgraph.h:283: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:285: error: syntax error before '*' token /usr/local/include/ajgraph.h:285: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:287: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:291: error: syntax error before "xcentre" /usr/local/include/ajgraph.h:294: error: syntax error before "ajGraphTextLength" /usr/local/include/ajgraph.h:294: error: syntax error before "xx1" /usr/local/include/ajgraph.h:296: error: syntax error before "ajGraphTextHeight" /usr/local/include/ajgraph.h:296: error: syntax error before "xx1" /usr/local/include/ajgraph.h:297: error: syntax error before "ajGraphDistPts" /usr/local/include/ajgraph.h:297: error: syntax error before "xx1" /usr/local/include/ajgraph.h:298: error: syntax error before "ajGraphFitTextOnLine" /usr/local/include/ajgraph.h:298: error: syntax error before "xx1" /usr/local/include/ajgraph.h:302: error: syntax error before "xcentre" make[1]: *** [clique.o] Error 1 make[1]: Leaving directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' make: *** [all-recursive] Error 1 Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately. Unauthorised use, disclosure, copying or alteration of this message is forbidden & may be unlawful. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute. This email, and associated attachments, has been checked locally for viruses but we can accept no responsibility once it has left our systems. Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes. The Institute for Animal Health is a company limited by guarantee, registered in England no. 559784. The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From ajb at ebi.ac.uk Mon May 11 15:21:20 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 11 May 2009 16:21:20 +0100 (BST) Subject: [EMBOSS] Problems installing EMBASSY: /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> References: <8975119BCD0AC5419D61A9CF1A923E9507E27895@iahce2ksrv1.iah.bbsrc.ac.uk> Message-ID: <53068.86.26.12.63.1242055280.squirrel@webmail.ebi.ac.uk> Hi Mick, It looks, from the following: > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory that you may have an old installation of EMBOSS under /usr/local (or bits of an old installation) i.e. it is looking in /usr/local/include rather than /usr/local/EMBOSS/include. The gcc compiler will usually look under /usr/include and /usr/local/include automatically and preferentially, so anything there will tend to override anything in /usr/local/EMBOSS/include. It is also unusual to see "-I/usr/include//include" there (perhaps a rogue CFLAGS environment variable somewhere or some manual editing of the makefiles), but the definition is meaningless and harmless (unless someone has been installing software under /usr/include). plplot.h is provided as part of the EMBOSS distribution (usually in /fu/bar/emboss/include/eplplot) and contains definitions for the graphics system. HTH Alan > Hi > > > > I am running RHEL 4 and just installed EMBOSS 6.0.1 in /usr/local/EMBOSS > > > > I downloaded ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.67.tar.gz > and tried to install that. > > > > I used ./configure --prefix=/usr/local/EMBOSS and then tried make. The > results are below. > > > > Any help? What is plplot.h? > > > > Thanks > > Mick > > > > -bash-3.00# make > > Making all in src > > make[1]: Entering directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIPNEW\" > -DVERSION=\"3.67\" -DSTDC_HEADER > > S=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_STDINT_H=1 -DHAVE_UNISTD_H=1 > > -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 > -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 > -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_ > > FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 > -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. > -I../include -I/usr/local/EMBOSS/incl > > ude -I/usr/local/EMBOSS/include/eplplot -DAJ_LinuxLF > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE > -DLENDIAN -I/usr/include//include -DNO_AUTH -O2 -MT > > clique.o -MD -MP -MF .deps/clique.Tpo -c -o clique.o clique.c > > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:29:20: plplot.h: No such file or directory > > In file included from /usr/local/include/emboss.h:5, > > from ../include/phylip.h:30, > > from clique.c:1: > > /usr/local/include/ajgraph.h:81: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:82: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:84: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:115: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:116: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:117: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:135: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:146: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:147: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:162: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:169: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:170: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:172: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:173: error: syntax error before "xx0" > > /usr/local/include/ajgraph.h:189: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:191: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:192: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:193: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:194: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:196: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:198: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:200: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:203: error: syntax error before "PLFLT" > > /usr/local/include/ajgraph.h:283: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:285: error: syntax error before '*' token > > /usr/local/include/ajgraph.h:285: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:287: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:291: error: syntax error before "xcentre" > > /usr/local/include/ajgraph.h:294: error: syntax error before > "ajGraphTextLength" > > /usr/local/include/ajgraph.h:294: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:296: error: syntax error before > "ajGraphTextHeight" > > /usr/local/include/ajgraph.h:296: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:297: error: syntax error before > "ajGraphDistPts" > > /usr/local/include/ajgraph.h:297: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:298: error: syntax error before > "ajGraphFitTextOnLine" > > /usr/local/include/ajgraph.h:298: error: syntax error before "xx1" > > /usr/local/include/ajgraph.h:302: error: syntax error before "xcentre" > > make[1]: *** [clique.o] Error 1 > > make[1]: Leaving directory `/usr/bioinfvm/PHYLIPNEW-3.67/src' > > make: *** [all-recursive] Error 1 > > > > Head of Bioinformatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > > > Please consider the environment and don't print this e-mail unless you > really need to. > > The information contained in this message may be confidential or legally > privileged and is intended solely for the addressee. If you have > received this message in error please delete it & notify the originator > immediately. Unauthorised use, disclosure, copying or alteration of > this message is forbidden & may be unlawful. The contents of this > e-mail are the views of the sender and do not necessarily represent the > views of the Institute. This email, and associated attachments, has > been checked locally for viruses but we can accept no responsibility > once it has left our systems. Communications on Institute computers are > monitored to secure the effective operation of the systems and for other > lawful purposes. > > > > The Institute for Animal Health is a company limited by guarantee, > registered in England no. 559784. > > The Institute is also a registered charity, Charity Commissioners > Reference No. 228824 > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From uludag at ebi.ac.uk Mon May 11 15:36:12 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Mon, 11 May 2009 16:36:12 +0100 Subject: [EMBOSS] [Taverna-users] Bootstrap In-Reply-To: <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it> <1241626362.1002.107.camel@emboss2.ebi.ac.uk><4A042DB0.9060403@ebi.ac.uk> <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> Message-ID: <1242056172.30340.192.camel@emboss2.ebi.ac.uk> Hi Achille, > - the fneighbor app fails everytime with errors like this : > Error: Distances file found 0 rows, expected 15 This problem looks like have been fixed in CVS version of EMBOSS, as i get reasonable output when i run CVS version of fneighbor with your input file. This suggests current patches don't include the fixes I thought they have. It is my fault that i didn't double check it before returning you. > I don't understand the "Standard error stream" explanation! about datafile > and the "-auto" param. "-auto" is an emboss parameter which means EMBOSS should try runing an application without asking further questions but using the inputs/parameters available on the command line. We will consider removing it from Soaplab job reports. "Standard error stream" is a term used by Soaplab meaning "error output of the job", it looks like we can improve its wording. > Instead If I use, for exsample, a 48 sequences alignment input I have a > java heap space error (is it my computer fault?). This is most probably related to memory used by your Taverna Java process. I tested your 48 sequence alignment with all 3 workflows attached, i didn't get any memory errors but i use a quite generous -Xmx setting in my runme.sh file. You may try increasing the default -Xmx setting in your taverna runme.sh file. Alternatively, as far as i know memory used grows each time i run a new workflow in taverna, you may try closing existing workflow run tabs before running a new workflow. > -the timeout limit for the jobs is 60 minutes!? , it is a restriction of > EBI that is impossible to avoid I suppose! this was a good enough timeout limit previously, i think we can increase it, let me discuss this with relevant people, if i execute the same fproml job outside LSF it takes about 80 minutes which suggests a 2 hour limit should allow your fproml jobs completed. > for example a fproml job with 48 seq align is more than 60 minutes long I > think because after 1 hour it returns a completed job message with empty > output. This is a bug in Soaplab (introduced by me), it should report the status terminated, rather than completed successfully. Regards, Mahmut From maoj at helix.nih.gov Tue May 12 14:11:20 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Tue, 12 May 2009 10:11:20 -0400 Subject: [EMBOSS] Error in edialign Message-ID: <4A098388.6070900@helix.nih.gov> Hi, When I run emboss-6.0.1 'edialign' program on command line, I saw this error: Error: File /usr/local/EMBOSS-6.0.1/share/EMBOSS/acd/edialign.acd line 124: (outseq) Attribute 'aligned' unknown The edialign.acd file was attached. Thank you. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: edialign.acd URL: From ajb at ebi.ac.uk Tue May 12 15:22:34 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 12 May 2009 16:22:34 +0100 (BST) Subject: [EMBOSS] Error in edialign In-Reply-To: <4A098388.6070900@helix.nih.gov> References: <4A098388.6070900@helix.nih.gov> Message-ID: <42293.86.26.12.63.1242141754.squirrel@webmail.ebi.ac.uk> Hi Jean, That problem was addressed by a recent patch put on the ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ Let us know if it doesn't fix it for you. HTH Alan > Hi, > > When I run emboss-6.0.1 'edialign' program on command line, I saw this > error: > Error: File /usr/local/EMBOSS-6.0.1/share/EMBOSS/acd/edialign.acd line > 124: (outseq) Attribute 'aligned' unknown > > The edialign.acd file was attached. > > Thank you. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From jerome at ibt.unam.mx Wed May 13 22:34:26 2009 From: jerome at ibt.unam.mx (Jerome) Date: Wed, 13 May 2009 17:34:26 -0500 Subject: [EMBOSS] fdnadist and fneighbor issue Message-ID: <4A0B4AF2.4080006@ibt.unam.mx> Dear all I'm using emboss 5.0 version, and come out of some problem. I've got a alignment of 15 dna sequence, generated by clustalw (emma). Thsi file is in fatsa format. I want to calculate the distance between all of this using fdnadist: $fdnadist -sequence globin-align.fasta -method f -outfile globin.fnadist All run without problem, and my output file is like this: 15 CHIHBA1 0.000000 0.010022 0.264744 0.167372 0.315764 0.319542 0.394008 0.397425 0.500520 0.498700 0.696916 1.352558 1.223696 1.327388 1.223196 CHIHBB1 0.010022 0.000000 0.226115 0.171012 0.318000 0.321806 0.403662 0.403176 0.510729 0.508896 0.696097 1.333125 1.241254 ../.. This file format seems to generate a issu with fneighbor, as it complains about 0 rows found in place of 15: $ fneighbor -datafile globin.fnadist -outfile globin.fneighbor Phylogenies from distance matrix by N-J or UPGMA method Error: Distances file found 0 rows, expected 15 Error: Unable to read distances file 'globin.fnadist' Died: fneighbor terminated: Bad value for '-datafile' and no prompt This problem disapeared if i format the distance file in one line for each sequence. As i do all of this command as default, maybe i forgot a option in the fdnadist ? This command is inside a flow of cemboss commands, so it's complicated for me to edit by hand each distance file to be "correct" for fneighbor.. Someone can explain me where i'm wrong? Regards -- -- J?r?me Moi j'aime bien quand M. Bl?durt raconte ses histoires de guerre, une fois il m'a expliqu? comment il a captur?, tout seul, un sous-marin pleins d'ennemis. (Histoires in?dites du Petit Nicolas, Goscinny & Semp?) From michael.watson at bbsrc.ac.uk Thu May 14 11:47:09 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu, 14 May 2009 12:47:09 +0100 Subject: [EMBOSS] fdnaml prompts for (optional) Phylip tree from command line Message-ID: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> Hi Running Emboss 6.01 with PHYLIPNEW installed (3.67) When I run fdnaml from the command line it always prompts for a philip tree, which is supposedly optional. I know from the docs I should be able to turn this off using -options but I can't find out what I can say to -options to make it stop. fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree -options=F Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): fdnaml -sequence=/tmp/18702.msf -outfile=stdout -outtreefile=/tmp/dummy.tree -options=0 Estimates nucleotide phylogeny by maximum likelihood Phylip tree file (optional): Please forgive me if I'm doing something silly.... Mick Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately. Unauthorised use, disclosure, copying or alteration of this message is forbidden & may be unlawful. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute. This email, and associated attachments, has been checked locally for viruses but we can accept no responsibility once it has left our systems. Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes. The Institute for Animal Health is a company limited by guarantee, registered in England no. 559784. The Institute is also a registered charity, Charity Commissioners Reference No. 228824 From pmr at ebi.ac.uk Thu May 14 12:35:51 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 14 May 2009 13:35:51 +0100 Subject: [EMBOSS] fdnaml prompts for (optional) Phylip tree from command line In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> References: <8975119BCD0AC5419D61A9CF1A923E9507E27929@iahce2ksrv1.iah.bbsrc.ac.uk> Message-ID: <4A0C1027.3040205@ebi.ac.uk> michael watson (IAH-C) wrote: > When I run fdnaml from the command line it always prompts for a philip > tree, which is supposedly optional. You can just hit return - if you do not give a tree file it will be ignored. You can also use -auto to accept the defaults for any other options. You can also put -nointreefile or -intreefile "" or -intreefile="" on the command line. "(optional)" in the prompt is just for information, there is nothing automatic about it. Perhaps we can find a standard way to say that an empty value is accepted (in the ACD file it has nullok set true). Hope that helps, Peter From pmr at ebi.ac.uk Fri May 15 10:15:26 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 15 May 2009 11:15:26 +0100 Subject: [EMBOSS] fdnadist and fneighbor issue In-Reply-To: <4A0B4AF2.4080006@ibt.unam.mx> References: <4A0B4AF2.4080006@ibt.unam.mx> Message-ID: <4A0D40BE.3010607@ebi.ac.uk> Dear Jerome, > I'm using emboss 5.0 version, and come out of some problem. > I've got a alignment of 15 dna sequence, generated by clustalw (emma). > > This file format seems to generate a issu with fneighbor, as it > complains about 0 rows found in place of 15: > > This problem disapeared if i format the distance file in one line for > each sequence. As i do all of this command as default, maybe i forgot a > option in the fdnadist ? This command is inside a flow of cemboss > commands, so it's complicated for me to edit by hand each distance file > to be "correct" for fneighbor.. There is a known problem with distance file formats. For EMBOSS 6.0.1 there is a patch available to correct the ajphylo.c source file. I am working through updating to phylip 3.68 and there are some new format issues with distance matrix files. They will be included in the July release. If you need a fix for EMBOSS 5.0 then we can try sending you a corrected 5.0 ajphylo.c source file. Hope this helps, Peter From achille.zappa at istge.it Mon May 11 13:04:26 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Mon, 11 May 2009 15:04:26 +0200 (CEST) Subject: [EMBOSS] Bootstrap In-Reply-To: <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> References: <2001.10.2.0.90.1241514253.squirrel@webmail.istge.it><1241626362.1002.107.camel@emboss2.ebi.ac.uk><4A042DB0.9060403@ebi.ac.uk> <60901.86.171.249.255.1241809405.squirrel@webmail.ebi.ac.uk> Message-ID: <4064.10.2.0.90.1242047066.squirrel@webmail.istge.it> > Hi Hamish, >> EMBOSS 6.0.1 install updated with current patches. > Thanks. > Achille, I would appreciate it if you can update your workflow to Soaplab > EMBOSS-6 services and check whether you now get correct results. Please > let us know if you still get erroneous results. > Regards, > Mahmut HI I made some tests with EMBOSS-6 apps in Taverna 1.7.1, but i had bad result, problably my faults because I haven't still exactly understand how to use them. I'll try to explain my doubts, sorry if it could be a little confused : primarly my objective is to create phylogenetic trees of protein sequences, so i use FASTA sequences for -> multiple alignments tolls to -> create phylo trees with distance matrix (nj and/or UPGMA) or Maximum Likelihood tools. For this I implemented in my workflow also a part like that in the attach files : - are the construction of the workflow, and connection links right? - the fneighbor app fails everytime with errors like this : " Soaplab call returned an error : Summary: Completed: Erroneously Report: Some error messages were reported. Name: phylogeny_distance_matrix.fneighbor Job ID: [phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 Program and parameters: /ebi/extserv/bin/EMBOSS-6.0.1/bin/fneighbor -datafile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/i_datafile -outfile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/o_outfile -outtreefile /ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 /o_outtreefiletreefile -auto --- end of parameters Exit code: 1 Standard error stream: Error: Distances file found 0 rows, expected 15 Error: Unable to read distances file '/ebi/extserv/soaplab- work/soaplab2_emboss6/SANDBOX /[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0 /i_datafile' Died: fneighbor terminated: Bad value for '-datafile' with -auto defined
SoaplabTask.execute(..) : line 146 <SoaplabTask.java>
ProcessorTask.runAndGenerateTemplates(..) : line 576 <ProcessorTask.java>
ProcessorTask.doInvocationWithRetryLogic(..) : line 517 <ProcessorTask.java>
ProcessorTask.invokeOnce(..) : line 436 <ProcessorTask.java>
ProcessorTask.invokeWithoutIteration(..) : line 642 <ProcessorTask.java>
ProcessorTask.invoke(..) : line 353 <ProcessorTask.java>
ProcessorTask.handleRun(..) : line 280 <ProcessorTask.java>
NewState$1.run(..) : line 67 <NewState.java>
] " I don't understand the "Standard error stream" explanation! about datafile and the "-auto" param. In attach also some input samples. Instead If I use, for exsample, a 48 sequences alignment input I have a java heap space error (is it my computer fault?). -the timeout limit for the jobs is 60 minutes!? , it is a restriction of EBI that is impossible to avoid I suppose! for example a fproml job with 48 seq align is more than 60 minutes long I think because after 1 hour it returns a completed job message with empty output. I apologize if all this stuff is only a my fault becuase of my ignorance about these processes but I will appreciate your help and advices. Thank you all for your time and disponibility BEST REGARDS CHEERS Achille P.S. Do you have some advices about the best tools for a phylogenetic tree research, about different alignment apps (ClustalW, Muscle, T-coffee, ....) different distance algorythm (NJ, UPGMA, MAX Likelihood, ....), tree constuction, computational optimization ... THANKS -- Achille Zappa -Bioinformatics National Cancer Research Institute (IST) Largo Benzi 10 16132 Genova - ITALY Tel. 010 5737288 -IEIIT - Sezione di Genova National Research Council (CNR) via De Marini, 6 16149 Genova - ITALY Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it -------------- next part -------------- A non-text attachment was scrubbed... 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Name: Muscle_Alignment.text URL: From karenryder1 at yahoo.com Wed May 20 02:26:02 2009 From: karenryder1 at yahoo.com (Karen Ryder) Date: Tue, 19 May 2009 19:26:02 -0700 (PDT) Subject: [EMBOSS] Program does not show up in menu Message-ID: <576741.76968.qm@web111615.mail.gq1.yahoo.com> I downloaded emboss from the synaptic package manager in Ubuntu (Jaunty) and it doesn't show up in the menu. I did a search for "emboss" in the filesystem, and found that some of the folders are in usr/share and in etc/ but I couldn't find the launch file. I have uninstall/reinstall from the package manager and rebooted my laptop but still nothing changes. What do I do? From charles-listes-emboss at plessy.org Wed May 20 04:16:38 2009 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 20 May 2009 13:16:38 +0900 Subject: [EMBOSS] Program does not show up in menu In-Reply-To: <576741.76968.qm@web111615.mail.gq1.yahoo.com> References: <576741.76968.qm@web111615.mail.gq1.yahoo.com> Message-ID: <20090520041637.GA14310@kunpuu.plessy.org> Le Tue, May 19, 2009 at 07:26:02PM -0700, Karen Ryder a ?crit : > I downloaded emboss from the synaptic package manager in Ubuntu (Jaunty) and > it doesn't show up in the menu. I did a search for "emboss" in the > filesystem, and found that some of the folders are in usr/share and in etc/ > but I couldn't find the launch file. I have uninstall/reinstall from the > package manager and rebooted my laptop but still nothing changes. What do I > do? Dear Karen, EMBOSS is a suite of command line programs, so they will not be seen from the menu of your graphical session. If you look for an interface packaged in Ubuntu, then I would like to suggets ?EMBOSS Explorer? (package emboss-explorer). Alternatively, you can try Jemboss, but this package is still very untested (feedback welcome!) and was never part of a stable Debian release (the EMBOSS packages on Ubuntu are originally made for Debian). If there are other interfaces that you are used to and would like to suggest for packaging, please do not hesitate to let me know. I was considering EMBOSS-kaptain, but I am affraid that both projects (EMBOSS-kaptain and Kaptain itself) are inactive for a long time, and I do not know how well they would work with KDE?4? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From Veronique.Martin at jouy.inra.fr Mon May 25 14:22:46 2009 From: Veronique.Martin at jouy.inra.fr (Veronique.Martin at jouy.inra.fr) Date: Mon, 25 May 2009 16:22:46 +0200 (CEST) Subject: [EMBOSS] whichdb error Message-ID: Hi all, I have this error with whichdb command: ----------- whichdb -showall Search all sequence databases for an entry and retrieve it ID or Accession number: L07770 Output file [stdout]: # Trying 'gb_rod:l07770' # Failed 'gb_rod:l07770' # Trying 'gb_pln:l07770' # Failed 'gb_pln:l07770' # Trying 'gp_syn:l07770' # Failed 'gp_syn:l07770' # Trying 'gb_pri:l07770' # Failed 'gb_pri:l07770' # Trying 'genbankwgs:l07770' # Failed 'genbankwgs:l07770' # Trying 'nr80:l07770' # Failed 'nr80:l07770' # Trying 'PRINTS:l07770' Warning: Cannot open division file '' for database 'PRINTS' Warning: seqCdQry failed # Failed 'PRINTS:l07770' # Trying 'opsdw:l07770' # Failed 'opsdw:l07770' # Trying 'emblwgs_hum:l07770' EMBOSS An error in ajindex.c at line 2429: GetKeys: No keys in node ------------ However, it's ok for this ID, because for example, infoseq or other commands (seqret...) runs correctly, as you can see bellow: ------------- infoseq genbank:l07770 Display basic information about sequences USA Database Name Accession Type Length %GC Description genbank-id:XELRHODOP genbank XELRHODOP L07770 N 1684 45.72 Xenopus laevis rhodopsin mRNA, complete cds. ------------- I run emboss 6.0.1 Any help? Thanks Veronique ------------------------------------------------- V?ronique MARTIN INRA - Unit? Math?matique, Informatique et G?nome 78352 Jouy-en Josas cedex tel.: 01 34 65 29 74 ------------------------------------------------- From noreply at netlogmail.com Tue May 26 04:44:14 2009 From: noreply at netlogmail.com (Duleep Samuel) Date: Tue, 26 May 2009 00:44:14 -0400 Subject: [EMBOSS] Visit my Netlog profile Message-ID: <200905260444.n4Q4iEWt014703@portal.open-bio.org> Hey, I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile. Take a look: http://en.netlog.com/go/mailurl/type=invite_1&mailid=319267176&id=1&url=-L2dvL3JlZ2lzdGVyL2lkPTEwODYwNTk3NzImaT10OTE_ Greetings, Duleep ---------------------------------------------------------------- Don't you wish to receive these e-mails? No longer wish to receive Netlog e-mails? http://en.netlog.com/go/mailurl/type=invite_1&mailid=319267176&id=2&url=-L2dvL25vbWFpbHMvaW52aXRlL2VtYWlsPS1aVzFpYjNOelFHeHBjM1J6TG05d1pXNHRZbWx2TG05eVp3X18mY29kZT0xMjEwMTAxMyZpZD0xMDg2MDU5NzcyJmk9dDky From pmr at ebi.ac.uk Tue May 26 20:07:13 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 26 May 2009 21:07:13 +0100 Subject: [EMBOSS] whichdb error In-Reply-To: References: Message-ID: <4A1C4BF1.2050507@ebi.ac.uk> Veronique.Martin at jouy.inra.fr wrote: > I have this error with whichdb command: Whichdb will search for L07770 by ID and by accession in all the databases you have defined. The outputn will show a list of all the databases it tests, which will be defined in your emboss.defaults file and perhaps in your personal ~/.embossrc file > ----------- > whichdb -showall > Search all sequence databases for an entry and retrieve it > ID or Accession number: L07770 > Output file [stdout]: > # Trying 'gb_rod:l07770' > # Failed 'gb_rod:l07770' > # Trying 'gb_pln:l07770' > # Failed 'gb_pln:l07770' > # Trying 'gp_syn:l07770' > # Failed 'gp_syn:l07770' > # Trying 'gb_pri:l07770' > # Failed 'gb_pri:l07770' > # Trying 'genbankwgs:l07770' > # Failed 'genbankwgs:l07770' > # Trying 'nr80:l07770' > # Failed 'nr80:l07770' > # Trying 'PRINTS:l07770' > Warning: Cannot open division file '' for database 'PRINTS' > Warning: seqCdQry failed This suggests you have PRINTS defined as a sequence database. Prints is a pattern database and does not need to be defined in emboss.defaults of ~/.embossrc > # Failed 'PRINTS:l07770' > # Trying 'opsdw:l07770' > # Failed 'opsdw:l07770' > # Trying 'emblwgs_hum:l07770' > > EMBOSS An error in ajindex.c at line 2429: > GetKeys: No keys in node > ------------ and this suggests a problem with the indexing of your emblwgs_hum database. You need to check the status of this database and correct it. Meanwhile, perhaps we can persuade whichdb to continue checking the remaining databases. You failed to find L07770 because it stopped at this point. > However, it's ok for this ID, because for example, > infoseq or other commands (seqret...) runs correctly, as you can see > bellow: > ------------- > infoseq genbank:l07770 > Display basic information about sequences > USA Database Name Accession Type > Length %GC Description > genbank-id:XELRHODOP genbank XELRHODOP L07770 N > 1684 45.72 Xenopus laevis rhodopsin mRNA, complete cds. So whichdb will find the entry when it reaches genbank and searched by accession. I hope this helps. Let us know (mail to emboss-bug at emboss.open-bio.org) if you need help in correcting your databases. regards, Peter Rice From maoj at helix.nih.gov Wed May 27 12:40:53 2009 From: maoj at helix.nih.gov (Jean Mao) Date: Wed, 27 May 2009 08:40:53 -0400 Subject: [EMBOSS] Alternative splicing applications in EMBOSS? Message-ID: <4A1D34D5.1000503@helix.nih.gov> Hi, I have tried to search EMBOSS to see if it has applications for alternative splicing analysis of a gene of interest but no luck. Just want to ask here in case I missed any. Thank you. Jean From pmr at ebi.ac.uk Wed May 27 13:06:52 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 27 May 2009 14:06:52 +0100 Subject: [EMBOSS] Alternative splicing applications in EMBOSS? In-Reply-To: <4A1D34D5.1000503@helix.nih.gov> References: <4A1D34D5.1000503@helix.nih.gov> Message-ID: <4A1D3AEC.2010206@ebi.ac.uk> Jean Mao wrote: > Hi, > > I have tried to search EMBOSS to see if it has applications for > alternative splicing analysis of a gene of interest but no luck. Just > want to ask here in case I missed any. Thank you. We are very interested in suggestions for new applications. What alternative splicing analysis do you need? regards, Peter