From felix.bemm at uni-wuerzburg.de Wed Jan 9 09:09:23 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:09:23 +0100 Subject: [maker-devel] Compilation Problems Message-ID: <50ED8823.8050001@uni-wuerzburg.de> Hi, I am trying to compile maker (2.27-beta) with MPI support on Ubuntu 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and a self compiled version (MPICH2 3.0.1) at hand. The latter one was compiled with the -enable-shared flag. I got the following error during the maker install command with both versions: Configuring MAKER with MPI support /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc MPI.c /software/mpich/bin/mpicc -c -I"/storage/software/intel64/maker-2.27-beta/src" -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c MPI.xs: In Funktion ?_MPI_Send?: MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? von inkompatiblem Zeigertyp [standardm??ig aktiviert] /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? erwartet, aber Argument hat Typ ?int *? Running Mkbootstrap for Parallel::Application::MPI () chmod 644 MPI.bs rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib -fstack-protector MPI.o -o blib/arch/auto/Parallel/Application/MPI/MPI.so \ \ /usr/bin/ld: /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when making a shared object; recompile with -fPIC /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read symbols: Bad value collect2: ld gab 1 als Ende-Status zur?ck make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make > out.make 2>&1 The build directory was: /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Application/MPI To debug the problem, cd to the build directory, and inspect the output files. at /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Application/MPI.pm line 223 Does anybody have an idea, what is happening here? Best regards Felix -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 09:18:06 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:18:06 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED8823.8050001@uni-wuerzburg.de> Message-ID: It is a problem with compilation of the shared libraries in MPICH2. You can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and CXXFLAGS environmental variables. Alternatively I would recommend not using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it is the new MPICH3. It is their first attempt to provide full support of the new MPI-3 standard, so compared to other MPICH2 releases which all use the MPI-2 standard it will be very buggy. So avoid it unless your inner geek loves the pain that comes from working with bleeding edge advances. I would recommend using the last release of MPICH2 which was version 1.5. Thanks, Carson On 13-01-09 10:09 AM, "Felix Bemm" wrote: >Hi, > >I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >a self compiled version (MPICH2 3.0.1) at hand. The latter one was >compiled with the -enable-shared flag. I got the following error during >the maker install command with both versions: > >Configuring MAKER with MPI support >/usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >"/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >MPI.c >/software/mpich/bin/mpicc -c >-I"/storage/software/intel64/maker-2.27-beta/src" >-I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >MPI.xs: In Funktion ?_MPI_Send?: >MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >von inkompatiblem Zeigertyp [standardm??ig aktiviert] >/usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >erwartet, aber Argument hat Typ ?int *? >Running Mkbootstrap for Parallel::Application::MPI () >chmod 644 MPI.bs >rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >/software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >-fstack-protector MPI.o -o >blib/arch/auto/Parallel/Application/MPI/MPI.so \ > \ > >/usr/bin/ld: >/storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >making a shared object; recompile with -fPIC >/storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >symbols: Bad value >collect2: ld gab 1 als Ende-Status zur?ck >make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 > >A problem was encountered while attempting to compile and install your >Inline >C code. The command that failed was: > make > out.make 2>&1 > >The build directory was: >/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >ion/MPI > >To debug the problem, cd to the build directory, and inspect the output >files. > > at >/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >tion/MPI.pm >line 223 > >Does anybody have an idea, what is happening here? > >Best regards >Felix > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From felix.bemm at uni-wuerzburg.de Wed Jan 9 09:53:21 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:53:21 +0100 Subject: [maker-devel] Compilation Problems In-Reply-To: References: Message-ID: <50ED9271.8090300@uni-wuerzburg.de> Thanks Carson, version change (to mpich2 1.5) fixed the problem. I did not realize that I was downloading some mpich3 after all. Thanks again for the fast help! Best regards Felix On 09.01.2013 16:18, Carson Holt wrote: > It is a problem with compilation of the shared libraries in MPICH2. You > can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and > CXXFLAGS environmental variables. Alternatively I would recommend not > using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it > is the new MPICH3. It is their first attempt to provide full support of > the new MPI-3 standard, so compared to other MPICH2 releases which all use > the MPI-2 standard it will be very buggy. So avoid it unless your inner > geek loves the pain that comes from working with bleeding edge advances. > I would recommend using the last release of MPICH2 which was version 1.5. > > Thanks, > Carson > > > On 13-01-09 10:09 AM, "Felix Bemm" wrote: > >> Hi, >> >> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >> compiled with the -enable-shared flag. I got the following error during >> the maker install command with both versions: >> >> Configuring MAKER with MPI support >> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >> MPI.c >> /software/mpich/bin/mpicc -c >> -I"/storage/software/intel64/maker-2.27-beta/src" >> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >> MPI.xs: In Funktion ?_MPI_Send?: >> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >> erwartet, aber Argument hat Typ ?int *? >> Running Mkbootstrap for Parallel::Application::MPI () >> chmod 644 MPI.bs >> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >> -fstack-protector MPI.o -o >> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >> \ >> >> /usr/bin/ld: >> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >> making a shared object; recompile with -fPIC >> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >> symbols: Bad value >> collect2: ld gab 1 als Ende-Status zur?ck >> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >> >> A problem was encountered while attempting to compile and install your >> Inline >> C code. The command that failed was: >> make > out.make 2>&1 >> >> The build directory was: >> /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >> ion/MPI >> >> To debug the problem, cd to the build directory, and inspect the output >> files. >> >> at >> /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >> tion/MPI.pm >> line 223 >> >> Does anybody have an idea, what is happening here? >> >> Best regards >> Felix >> >> -- >> Felix Bemm >> Department of Bioinformatics >> University of W?rzburg, Germany >> Tel: +49 931 - 31 83696 >> Fax: +49 931 - 31 84552 >> felix.bemm at uni-wuerzburg.de >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 09:49:51 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:49:51 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED9271.8090300@uni-wuerzburg.de> Message-ID: I'm Glad it worked. Thanks, Carson On 13-01-09 10:53 AM, "Felix Bemm" wrote: >Thanks Carson, > >version change (to mpich2 1.5) fixed the problem. I did not realize that >I was downloading some mpich3 after all. Thanks again for the fast help! > >Best regards >Felix > >On 09.01.2013 16:18, Carson Holt wrote: >> It is a problem with compilation of the shared libraries in MPICH2. You >> can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS >>and >> CXXFLAGS environmental variables. Alternatively I would recommend not >> using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it >> is the new MPICH3. It is their first attempt to provide full support of >> the new MPI-3 standard, so compared to other MPICH2 releases which all >>use >> the MPI-2 standard it will be very buggy. So avoid it unless your inner >> geek loves the pain that comes from working with bleeding edge advances. >> I would recommend using the last release of MPICH2 which was version >>1.5. >> >> Thanks, >> Carson >> >> >> On 13-01-09 10:09 AM, "Felix Bemm" wrote: >> >>> Hi, >>> >>> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >>> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >>> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >>> compiled with the -enable-shared flag. I got the following error during >>> the maker install command with both versions: >>> >>> Configuring MAKER with MPI support >>> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >>> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv >>>MPI.xsc >>> MPI.c >>> /software/mpich/bin/mpicc -c >>> -I"/storage/software/intel64/maker-2.27-beta/src" >>> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >>> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >>> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >>> MPI.xs: In Funktion ?_MPI_Send?: >>> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >>> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >>> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >>> erwartet, aber Argument hat Typ ?int *? >>> Running Mkbootstrap for Parallel::Application::MPI () >>> chmod 644 MPI.bs >>> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >>> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >>> -fstack-protector MPI.o -o >>> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >>> \ >>> >>> /usr/bin/ld: >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >>> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >>> making a shared object; recompile with -fPIC >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >>> symbols: Bad value >>> collect2: ld gab 1 als Ende-Status zur?ck >>> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >>> >>> A problem was encountered while attempting to compile and install your >>> Inline >>> C code. The command that failed was: >>> make > out.make 2>&1 >>> >>> The build directory was: >>> >>>/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applic >>>at >>> ion/MPI >>> >>> To debug the problem, cd to the build directory, and inspect the output >>> files. >>> >>> at >>> >>>/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Appli >>>ca >>> tion/MPI.pm >>> line 223 >>> >>> Does anybody have an idea, what is happening here? >>> >>> Best regards >>> Felix >>> >>> -- >>> Felix Bemm >>> Department of Bioinformatics >>> University of W?rzburg, Germany >>> Tel: +49 931 - 31 83696 >>> Fax: +49 931 - 31 84552 >>> felix.bemm at uni-wuerzburg.de >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From ranjani at uga.edu Wed Jan 16 10:16:27 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 16 Jan 2013 16:16:27 +0000 Subject: [maker-devel] Transcriptome data to gene models Message-ID: Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Wed Jan 16 11:19:13 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 16 Jan 2013 17:19:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Wed Jan 16 11:24:08 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 16 Jan 2013 17:24:08 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From barry.moore at genetics.utah.edu Wed Jan 16 12:07:57 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 16 Jan 2013 10:07:57 -0800 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> Message-ID: Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Jan 16 12:16:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 16 Jan 2013 13:16:15 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Wed Jan 16 12:26:12 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Wed, 16 Jan 2013 18:26:12 +0000 Subject: [maker-devel] Txome annotation Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA0415B8DE@EXCHANGE-05.internal.solazyme.com> Does anyone have a good suggestion for annotating transcriptomes? In particular calling ORFs (like the best ORF, not just a simple longest ORF) and doing functional annotation? I am currently using cd-hit to try and get a representative transcript set, but I want somthing similar in the ORF space that attempts to call the best, and alternative, ORFs. I am using AutoFact to do functional annotation, and it works, but I don't think it is under continued development. Thanks, Shane ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of maker-devel-request at yandell-lab.org [maker-devel-request at yandell-lab.org] Sent: Wednesday, January 16, 2013 10:16 AM To: maker-devel at yandell-lab.org Subject: maker-devel Digest, Vol 56, Issue 2 Send maker-devel mailing list submissions to maker-devel at yandell-lab.org To subscribe or unsubscribe via the World Wide Web, visit http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org or, via email, send a message with subject or body 'help' to maker-devel-request at yandell-lab.org You can reach the person managing the list at maker-devel-owner at yandell-lab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of maker-devel digest..." Today's Topics: 1. Transcriptome data to gene models (Sivaranjani Namasivayam) 2. Re: Transcriptome data to gene models (Daniel Ence) 3. Re: Transcriptome data to gene models (Fields, Christopher J) 4. Re: Transcriptome data to gene models (Barry Moore) 5. Re: Transcriptome data to gene models (Carson Holt) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Jan 2013 16:16:27 +0000 From: Sivaranjani Namasivayam To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 16 Jan 2013 17:19:13 +0000 From: Daniel Ence To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 16 Jan 2013 17:24:08 +0000 From: "Fields, Christopher J" To: Daniel Ence Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF at CHIMBX5.ad.uillinois.edu> Content-Type: text/plain; charset="iso-8859-1" I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org ------------------------------ Message: 4 Date: Wed, 16 Jan 2013 10:07:57 -0800 From: Barry Moore To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 16 Jan 2013 13:16:15 -0500 From: Carson Holt To: Barry Moore , Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org End of maker-devel Digest, Vol 56, Issue 2 ****************************************** From kapeelc at gmail.com Fri Jan 18 13:00:42 2013 From: kapeelc at gmail.com (Kapeel Chougule) Date: Fri, 18 Jan 2013 12:00:42 -0700 Subject: [maker-devel] BLAST options error Message-ID: Hi, I had this error for one of the chromosomes: BLAST options error: /opt/kapeel/maker_runs/leersia/chr11/Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/comp84263_c0_seq4.for_blastn.fasta does not match input format type, default input type is FASTA ERROR: Failed while collecting blastn reports ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:Chr11 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:Chr11 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/Chr11.286769.311208.0.comp84263_c0_seq4%2Efor_blastn%2Efasta.blastn did not finish on the last run and must be erased Maker is now finished!!! I checked the comp84263_c0_seq4.for_blastn.fasta file for any spaces before > symbol in the header section, it seems to be ok with that. Any suggestions? Thank you, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu From mikael.durling at slu.se Tue Jan 22 03:56:45 2013 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 22 Jan 2013 09:56:45 +0000 Subject: [maker-devel] maker_map_ids anomaly Message-ID: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Hi, I'm trying to load maker annotations into JBrowse, however, the flat file loader can't parse the maker gff stating "parse error: orphans". Looking into one of the broken maker transcripts, it looks like below. Note that the two different mRNAs get the same ID, but a different name. The lines from maker_map_ids are pasted below too. This was a re-annotation run of a previous maker run, which was id_mapped before being used as maker_gff in the current run with model_pass=1 in order to preserve gene names. (btw, loading the unmapped initial maker run into jbrowse works fine.) scf_89829 maker gene 38002 41976 . + . ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; scf_89829 maker mRNA 38002 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=CROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=436|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; scf_89829 maker mRNA 38611 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=maker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33|3|1149|602;_eAED=0.06;Note=Protein of unknown function; scf_89829 maker exon 38002 38349 . + . ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; scf_89829 maker exon 38872 39702 . + . ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 39762 41976 . + . ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 38611 38647 . + . ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38002 38349 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38611 38647 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; Related id map lines: CROS1_G00002820 CROS1_G00002820 maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 CROS1_T00002820_1 CROS1_T00002820_2 and the command line for maker_map_ids: maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ --iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > CrosV1.maker.output/CrosV1.id_map thanks for any hints, Mikael From carsonhh at gmail.com Wed Jan 23 08:42:08 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:42:08 -0700 Subject: [maker-devel] maker_map_ids anomaly In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Message-ID: So does the problem occur immediately following the maker_map_ids step or does it occur after running maker before the maker_map_ids step. I ask so I can identify if it is the maker_map_ids script I neeed to debug or maker. Could you send me the GFF3 file imediatley preceding the step where the error originate. Thanks, Carson On 13-01-22 2:56 AM, "Mikael Brandstr?m Durling" wrote: >Hi, > >I'm trying to load maker annotations into JBrowse, however, the flat file >loader can't parse the maker gff stating "parse error: orphans". Looking >into one of the broken maker transcripts, it looks like below. Note that >the two different mRNAs get the same ID, but a different name. The lines >from maker_map_ids are pasted below too. This was a re-annotation run of >a previous maker run, which was id_mapped before being used as maker_gff >in the current run with model_pass=1 in order to preserve gene names. >(btw, loading the unmapped initial maker run into jbrowse works fine.) > >scf_89829 maker gene 38002 41976 . + . >ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; >scf_89829 maker mRNA 38002 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=C >ROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=4 >36|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; >scf_89829 maker mRNA 38611 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=m >aker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33| >3|1149|602;_eAED=0.06;Note=Protein of unknown function; >scf_89829 maker exon 38002 38349 . + . >ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; >scf_89829 maker exon 38872 39702 . + . >ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 39762 41976 . + . >ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 38611 38647 . + . >ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38002 38349 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38611 38647 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; > > >Related id map lines: > >CROS1_G00002820 CROS1_G00002820 >maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 >CROS1_T00002820_1 CROS1_T00002820_2 > > >and the command line for maker_map_ids: > >maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ >--iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > >CrosV1.maker.output/CrosV1.id_map > >thanks for any hints, >Mikael >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Wed Jan 23 08:59:39 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:59:39 -0700 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Wed Jan 23 09:31:46 2013 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 23 Jan 2013 10:31:46 -0500 Subject: [maker-devel] Question about AED scores Message-ID: Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the *_AED* attribute, which leads to my other question: what does the value of the *_eAED* attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Wed Jan 23 13:42:42 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Wed, 23 Jan 2013 14:42:42 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Message-ID: <51003D32.4080908@jcvi.org> Hello, I'm trying to use the MAKER pipeline to calculate AED scores for the gene models coming out of our annotation pipeline (EVidence Modeler). We then want to compare these computed AED scores with those computed for the gene models coming out of the MAKER2 pipeline. For this purpose, I configured the maker_opts.ctl file like so: 1) Specify gff file coming from our annotation pipeline using `model_gff` param 2) Specify gff file containing est2genome results (computed using MAKER2) using the `est_gff` param 3) Specify gff file containing protein2genome results (computed using MAKER2) using the `protein_gff` param 4) Specify the genome fasta sequence file using the `genome` param I recently configured MAKER 2.27b to work using MPI and I tried launching one contig (chromosome) on a compute node spawning 12 processes like so: mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err Side note: Without MPI, it works fine but takes very very long to complete running on one chromosome (since it is going through the chunks serially). On inspecting the `maker.err` file, I see server error messages that say `DBD::SQLite::db do failed: database is locked`. On referring to a previous email thread on the `maker-devel` mailing list, I see that Carson had replied to the person with a similar issue asking them to check if the working directory and TMP directory are being mounted on an NFS filesystem because this is a potential problem with SQLite databases. Based on that suggestion, I switched the TMP directory to use a local filesytem but the working directory is still NFS mounted. Despite that, I still get this error. The previous email thread had no resolution for this issue. My question is, should the working directory be local as well? I see that despite setting the `TMP` variable, the SQLite DB is getting created in the working directory. What might be the issue? Also, apart from this one error, I notice another error: ERROR: Non-unique top level ID for chr5:hit:1454:4_0 While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. On inspecting the input GFF file (protein2genome), I see that this ID is never repeated. So I have no idea whats going on here either. Any suggestions? Below is my `maker.err` file from the run. (Dropbox link) Thank you very much. Best, Vivek -- Vivek Krishnakumar vkrishnakumar at jcvi.org I've linked 1 file to this email: maker.err (97.7 MB)Dropbox http://db.tt/2tYyKCD7 Mozilla Thunderbird makes it easy to share large files over email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: attachment-24.png Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dropbox.png Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 13:02:12 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 14:02:12 -0500 Subject: [maker-devel] Question about AED scores In-Reply-To: Message-ID: AED from MAKER in the based on nucleotide-level congruency of the transcript compared to the collapsed evidence. eAED is also at the nucleotide level but is adjusted for inferred support of exons, such as can happen with mRNAseq (I.e. I can confirm the splice sites at each end but as the exon gets longer the middle is less likely to be covered). So if I can infer the middle based on ORF and the splice site are confirmed then I consider the middle of the exon to be confirmed for calculating eAED. eAED also adjusts for reading frame from protein evidence alignments, i.e. protein overlap in a different reading frame than the final gene model will not contribute to eAED. So because of this, eAED takes much longer to calculate but is sometimes more useful. Much of the time AED and eAED are identical. Thanks, Carson From: Daniel Standage Date: Wednesday, 23 January, 2013 10:31 AM To: Maker Mailing List Subject: [maker-devel] Question about AED scores Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the _AED attribute, which leads to my other question: what does the value of the _eAED attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Thu Jan 24 13:49:36 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Thu, 24 Jan 2013 14:49:36 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51003D32.4080908@jcvi.org> References: <51003D32.4080908@jcvi.org> Message-ID: <51019050.1030003@jcvi.org> Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the > gene models coming out of our annotation pipeline (EVidence Modeler). > We then want to compare these computed AED scores with those computed > for the gene models coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using > `model_gff` param > 2) Specify gff file containing est2genome results (computed using > MAKER2) using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using > MAKER2) using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried > launching one contig (chromosome) on a compute node spawning 12 > processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to > complete running on one chromosome (since it is going through the > chunks serially). > > On inspecting the `maker.err` file, I see server error messages that > say `DBD::SQLite::db do failed: database is locked`. On referring to a > previous email thread on the `maker-devel` mailing list, I see that > Carson had replied to the person with a similar issue asking them to > check if the working directory and TMP directory are being mounted on > an NFS filesystem because this is a potential problem with SQLite > databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite > that, I still get this error. The previous email thread had no > resolution for this issue. My question is, should the working > directory be local as well? I see that despite setting the `TMP` > variable, the SQLite DB is getting created in the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID > is never repeated. So I have no idea whats going on here either. Any > suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > I've linked 1 file to this email: > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > Mozilla Thunderbird makes it easy to > share large files over email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 14:02:58 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:02:58 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51019050.1030003@jcvi.org> Message-ID: If you still see issue, let me know. I have a hard time seeing how just moving to MPICH2 would have solved the issue. It may also have been an initial problem with the first GFF# db being created and running on a new job recreated it correctly. Either way, let me know if it comes up on your bigger run. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 2:49 PM To: , Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the gene > models coming out of our annotation pipeline (EVidence Modeler). We then want > to compare these computed AED scores with those computed for the gene models > coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using `model_gff` > param > 2) Specify gff file containing est2genome results (computed using MAKER2) > using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using MAKER2) > using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried launching one > contig (chromosome) on a compute node spawning 12 processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to complete > running on one chromosome (since it is going through the chunks serially). > > On inspecting the `maker.err` file, I see server error messages that say > `DBD::SQLite::db do failed: database is locked`. On referring to a previous > email thread on the `maker-devel` mailing list, I see that Carson had replied > to the person with a similar issue asking them to check if the working > directory and TMP directory are being mounted on an NFS filesystem because > this is a potential problem with SQLite databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite that, I > still get this error. The previous email thread had no resolution for this > issue. My question is, should the working directory be local as well? I see > that despite setting the `TMP` variable, the SQLite DB is getting created in > the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID is > never repeated. So I have no idea whats going on here either. Any suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > > > I've linked 1 file to this email: > > > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > > > Mozilla Thunderbird makes it easy to share > large files over email. > > > _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From sbrubaker at solazyme.com Thu Jan 24 14:17:57 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:17:57 +0000 Subject: [maker-devel] Maker-P Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Hi, I heard about Maker-P at PAG. We are working on an algae, which is closer to plants than just about anything else - I am wondering, would Maker-P be useful for us to use instead of regular Maker? From carsonhh at gmail.com Thu Jan 24 14:31:28 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:31:28 -0500 Subject: [maker-devel] FW: Maker-P In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From michael.s.campbell1 at gmail.com Thu Jan 24 14:47:20 2013 From: michael.s.campbell1 at gmail.com (Michael Campbell) Date: Thu, 24 Jan 2013 13:47:20 -0700 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt wrote: > I'm forwarding this to the most relevant people. > > --Carson > > > On 13-01-24 3:17 PM, "Shane Brubaker" wrote: > > >Hi, I heard about Maker-P at PAG. We are working on an algae, which is > >closer to plants than just about anything else - I am wondering, would > >Maker-P be useful for us to use instead of regular Maker? > > > >_______________________________________________ > >maker-devel mailing list > >maker-devel at box290.bluehost.com > >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Thu Jan 24 14:48:19 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:48:19 +0000 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B23517@EXCHANGE-MB01.internal.solazyme.com> Ok that makes sense - Thanks! Sincerely, Shane Brubaker Director of BioInformatics Solazyme, Inc. 225 Gateway Blvd. S. San Francisco, CA 94080 From: Michael Campbell [mailto:michael.s.campbell1 at gmail.com] Sent: Thursday, January 24, 2013 12:47 PM To: Carson Holt Cc: Shane Brubaker; MeiYee Law; Mark Yandell; Maker Mailing List Subject: Re: FW: [maker-devel] Maker-P Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt > wrote: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" > wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 24 15:39:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 16:39:15 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <5101A7D6.4070101@jcvi.org> Message-ID: Done. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 4:29 PM To: Carson Holt Cc: "mcampbell at genetics.utah.edu" Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Ok. Seems to be working fine. I pointed the TMP parameter to our scratch area. Thanks for your suggestion. Should I forward this conversation thread to the maker-devel list ? Vivek On 01/24/2013 04:08 PM, Carson Holt wrote: > > SQLlite will choke almost immediately if it's not set up with the correct > flags, so you will know right away. > > > > > --Carson > > > > > From: "Krishnakumar, Vivek" > Date: Thursday, 24 January, 2013 3:35 PM > To: Carson Holt > Cc: "mcampbell at genetics.utah.edu" > Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked > (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI > > > > > > > Okay. I will try doing that. But how can I find out that my NFS mounted area > has -nolock set? The filesystem areas that we work on are managed by our IT > department. > > Thanks. > Vivek > > > On 01/24/2013 03:27 PM, Carson Holt wrote: > > >> >> If you don't have locally mounted space big enough, then just use an NFS >> mounted /TMP. You will take a slight performance hit, but it may still work >> if it is mounted with -nolock set so SQLite stops complaining. >> >> >> >> >> --Carson >> >> >> >> >> From: "Krishnakumar, Vivek" >> Date: Thursday, 24 January, 2013 3:24 PM >> To: Carson Holt >> Cc: "mcampbell at genetics.utah.edu" >> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >> >> >> >> >> >> >> I no longer see that warning. >> >> The only thing I see is that MAKER now complains that the DB is corrupt, and >> that is because I only have 5GB of /tmp space on the server I currently have >> access to and that is not enough for the whole genome FASTA + est2genome + >> protein2genome + model_gff (EVM). >> >> Thanks, >> Vivek >> >> >> >> On 01/24/2013 03:20 PM, Carson Holt wrote: >> >> >>> >>> You should be able to run on an NFS drive. After creating the initial >>> SQLite database, maker now gives each node it's own copy that is stored in >>> the TMP directory (should be local to each node). Could you send me the >>> GFF3 file that gives the warning, so I can look at it. >>> >>> >>> >>> >>> Thanks, >>> >>> Carson >>> >>> >>> >>> >>> >>> >>> >>> From: "Krishnakumar, Vivek" >>> Date: Thursday, 24 January, 2013 3:17 PM >>> To: Carson Holt >>> Cc: "mcampbell at genetics.utah.edu" >>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>> >>> >>> >>> >>> >>> >>> Hi Carson, >>> >>> I did make sure that every time I reran the pipeline, I deleted the >>> maker.output directory and the temporary files in /tmp. That way I know that >>> the DBs get created fresh. >>> >>> When it was openMPI based, I noticed that irrespective of whether I enabled >>> or disabled the `-TMP` parameter, I would get the database locked error. At >>> this point, mpicc was openMPI based and mpiexec (hydra) was MPICH2 based. >>> >>> On installing MPICH2 as a non-root user and rebuilding `maker`, this issue >>> vanished. Just an observation. >>> >>> The issue I have now with scaling up is that I do not currently have access >>> to a server that has a large amount of non-NFS mounted storage space (we do >>> have such a server but it has been reserved for a different project by a >>> group in our institute). Thus, the creation of the SQLite db is halted mid >>> way and now MAKER complains that the database is corrupt. I can either run >>> the chromosomes individually (serially) and then the scaffolds as one group >>> or wait to get a time slot of that server. >>> >>> Will let you know if I have any more issues. >>> >>> Thank you. >>> Vivek >>> >>> >>> >>> On 01/24/2013 03:02 PM, Carson Holt wrote: >>> >>> >>>> >>>> If you still see issue, let me know. I have a hard time seeing how just >>>> moving to MPICH2 would have solved the issue. It may also have been an >>>> initial problem with the first GFF# db being created and running on a new >>>> job recreated it correctly. Either way, let me know if it comes up on your >>>> bigger run. >>>> >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Carson >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> From: "Krishnakumar, Vivek" >>>> Date: Thursday, 24 January, 2013 2:49 PM >>>> To: , >>>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>>> >>>> >>>> >>>> >>>> >>>> >>>> Hi Everybody, >>>> >>>> Sorry for jumping the gun and writing to the mailing list before >>>> completely troubleshooting this issue. I was able to figure out the problem >>>> and get MAKER 2.27b working fine in MPI mode. >>>> >>>> The issue was with the incorrect version of mpicc (it was openMPI based >>>> and not mpich2). I was able to successfully run through the steps described >>>> below on one chromosome in under a few hours (~2). Now I'm scaling it to >>>> the whole genome (8 chromosomes and ~2200 unanchored scaffolds). >>>> >>>> Thank you. >>>> Vivek >>>> >>>> >>>> On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I'm trying to use the MAKER pipeline to calculate AED scores for the gene >>>>> models coming out of our annotation pipeline (EVidence Modeler). We then >>>>> want to compare these computed AED scores with those computed for the gene >>>>> models coming out of the MAKER2 pipeline. >>>>> >>>>> For this purpose, I configured the maker_opts.ctl file like so: >>>>> 1) Specify gff file coming from our annotation pipeline using `model_gff` >>>>> param >>>>> 2) Specify gff file containing est2genome results (computed using MAKER2) >>>>> using the `est_gff` param >>>>> 3) Specify gff file containing protein2genome results (computed using >>>>> MAKER2) using the `protein_gff` param >>>>> 4) Specify the genome fasta sequence file using the `genome` param >>>>> >>>>> I recently configured MAKER 2.27b to work using MPI and I tried launching >>>>> one contig (chromosome) on a compute node spawning 12 processes like so: >>>>> mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl >>>>> maker_exe.ctl 2>&1 | tee maker.err >>>>> >>>>> Side note: Without MPI, it works fine but takes very very long to >>>>> complete running on one chromosome (since it is going through the chunks >>>>> serially). >>>>> >>>>> On inspecting the `maker.err` file, I see server error messages that say >>>>> `DBD::SQLite::db do failed: database is locked`. On referring to a >>>>> previous email thread on the `maker-devel` mailing list, I see that Carson >>>>> had replied to the person with a similar issue asking them to check if the >>>>> working directory and TMP directory are being mounted on an NFS filesystem >>>>> because this is a potential problem with SQLite databases. >>>>> >>>>> Based on that suggestion, I switched the TMP directory to use a local >>>>> filesytem but the working directory is still NFS mounted. Despite that, I >>>>> still get this error. The previous email thread had no resolution for this >>>>> issue. My question is, should the working directory be local as well? I >>>>> see that despite setting the `TMP` variable, the SQLite DB is getting >>>>> created in the working directory. >>>>> >>>>> What might be the issue? >>>>> >>>>> Also, apart from this one error, I notice another error: >>>>> ERROR: Non-unique top level ID for chr5:hit:1454:4_0 >>>>> While this is technically legal in GFF3, it usually >>>>> indicates a poorly fomatted GFF3 file (perhaps you >>>>> tried to merge two GFF3 files without accounting for >>>>> unique IDs). MAKER will not handle these correctly. >>>>> >>>>> On inspecting the input GFF file (protein2genome), I see that this ID is >>>>> never repeated. So I have no idea whats going on here either. Any >>>>> suggestions? >>>>> >>>>> Below is my `maker.err` file from the run. (Dropbox link) >>>>> >>>>> Thank you very much. >>>>> Best, >>>>> >>>>> Vivek >>>>> >>>>> -- >>>>> Vivek Krishnakumar >>>>> vkrishnakumar at jcvi.org >>>>> >>>>> >>>>> >>>>> I've linked 1 file to this email: >>>>> >>>>> >>>>> maker.err (97.7 MB)Dropbox >>>>> http://db.tt/2tYyKCD7 >>>>> >>>>> >>>>> Mozilla Thunderbird makes it easy to >>>>> share large files over email. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> _______________________________________________ maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >>> >> >> >> >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From ranjani at uga.edu Thu Jan 24 23:17:13 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Fri, 25 Jan 2013 05:17:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: , Message-ID: I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam > Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" > Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 12:43:17 2013 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2013 13:43:17 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Also since single exon ESTs are almost always coming from background transcription and not real genes, MAKER may also require some sort of protein alignment or ab initio predictor support before promoting them to gene models. --Carson From: Sivaranjani Namasivayam Date: Friday, 25 January, 2013 12:17 AM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] Transcriptome data to gene models I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Tue Jan 29 10:50:24 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 29 Jan 2013 09:50:24 -0700 Subject: [maker-devel] Fwd: Help in installation of MAKER2 References: Message-ID: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 10:57:25 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 11:57:25 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: If it is a 64 bit Intel Mac make sure you install the 64 bit version of fink and not the 32 bit version. Then use fink to install both of these --> glib2-dev glib2-shlibs Installing them any other way on a Mac makes it so much harder to get the configuration right. Do 'fink remove' if you've already installed them with fink, then update fink and make sure it is the right fink for your processor before reinstalling. --Carson From: Barry Moore Date: Tuesday, 29 January, 2013 11:50 AM To: Maker Mailing List Cc: Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Jan 29 10:58:57 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 29 Jan 2013 16:58:57 +0000 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> References: , <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 Date: January 29, 2013 4:45:49 AM MST To: > Hi Barry, I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: checking for socklen_t... yes checking for pkg-config... no ERROR: Could not find pkg-config ... is glib-2 installed ??? macpro:exonerate-2.2.0 admin$ pkg-get -bash: pkg-get: command not found I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 11:04:54 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 12:04:54 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: Message-ID: I had problems moving from OS X 10.5 to 10.6 and from 10.6 to 10.7. All of which were solved by reinstalling fink (for the right processor ? 32bit vs 64bit) and all tools and libraries I had from fink. Thanks, Carson From: Daniel Ence Date: Tuesday, 29 January, 2013 11:58 AM To: Maker Mailing List , Carson Holt Cc: "alexmendozasoler at gmail.com" Subject: RE: [maker-devel] Fwd: Help in installation of MAKER2 Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:09:23 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:09:23 +0100 Subject: [maker-devel] Compilation Problems Message-ID: <50ED8823.8050001@uni-wuerzburg.de> Hi, I am trying to compile maker (2.27-beta) with MPI support on Ubuntu 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and a self compiled version (MPICH2 3.0.1) at hand. The latter one was compiled with the -enable-shared flag. I got the following error during the maker install command with both versions: Configuring MAKER with MPI support /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc MPI.c /software/mpich/bin/mpicc -c -I"/storage/software/intel64/maker-2.27-beta/src" -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c MPI.xs: In Funktion ?_MPI_Send?: MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? von inkompatiblem Zeigertyp [standardm??ig aktiviert] /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? erwartet, aber Argument hat Typ ?int *? Running Mkbootstrap for Parallel::Application::MPI () chmod 644 MPI.bs rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib -fstack-protector MPI.o -o blib/arch/auto/Parallel/Application/MPI/MPI.so \ \ /usr/bin/ld: /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when making a shared object; recompile with -fPIC /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read symbols: Bad value collect2: ld gab 1 als Ende-Status zur?ck make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make > out.make 2>&1 The build directory was: /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Application/MPI To debug the problem, cd to the build directory, and inspect the output files. at /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Application/MPI.pm line 223 Does anybody have an idea, what is happening here? Best regards Felix -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:18:06 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:18:06 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED8823.8050001@uni-wuerzburg.de> Message-ID: It is a problem with compilation of the shared libraries in MPICH2. You can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and CXXFLAGS environmental variables. Alternatively I would recommend not using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it is the new MPICH3. It is their first attempt to provide full support of the new MPI-3 standard, so compared to other MPICH2 releases which all use the MPI-2 standard it will be very buggy. So avoid it unless your inner geek loves the pain that comes from working with bleeding edge advances. I would recommend using the last release of MPICH2 which was version 1.5. Thanks, Carson On 13-01-09 10:09 AM, "Felix Bemm" wrote: >Hi, > >I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >a self compiled version (MPICH2 3.0.1) at hand. The latter one was >compiled with the -enable-shared flag. I got the following error during >the maker install command with both versions: > >Configuring MAKER with MPI support >/usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >"/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >MPI.c >/software/mpich/bin/mpicc -c >-I"/storage/software/intel64/maker-2.27-beta/src" >-I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >MPI.xs: In Funktion ?_MPI_Send?: >MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >von inkompatiblem Zeigertyp [standardm??ig aktiviert] >/usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >erwartet, aber Argument hat Typ ?int *? >Running Mkbootstrap for Parallel::Application::MPI () >chmod 644 MPI.bs >rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >/software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >-fstack-protector MPI.o -o >blib/arch/auto/Parallel/Application/MPI/MPI.so \ > \ > >/usr/bin/ld: >/storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >making a shared object; recompile with -fPIC >/storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >symbols: Bad value >collect2: ld gab 1 als Ende-Status zur?ck >make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 > >A problem was encountered while attempting to compile and install your >Inline >C code. The command that failed was: > make > out.make 2>&1 > >The build directory was: >/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >ion/MPI > >To debug the problem, cd to the build directory, and inspect the output >files. > > at >/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >tion/MPI.pm >line 223 > >Does anybody have an idea, what is happening here? > >Best regards >Felix > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:53:21 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:53:21 +0100 Subject: [maker-devel] Compilation Problems In-Reply-To: References: Message-ID: <50ED9271.8090300@uni-wuerzburg.de> Thanks Carson, version change (to mpich2 1.5) fixed the problem. I did not realize that I was downloading some mpich3 after all. Thanks again for the fast help! Best regards Felix On 09.01.2013 16:18, Carson Holt wrote: > It is a problem with compilation of the shared libraries in MPICH2. You > can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and > CXXFLAGS environmental variables. Alternatively I would recommend not > using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it > is the new MPICH3. It is their first attempt to provide full support of > the new MPI-3 standard, so compared to other MPICH2 releases which all use > the MPI-2 standard it will be very buggy. So avoid it unless your inner > geek loves the pain that comes from working with bleeding edge advances. > I would recommend using the last release of MPICH2 which was version 1.5. > > Thanks, > Carson > > > On 13-01-09 10:09 AM, "Felix Bemm" wrote: > >> Hi, >> >> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >> compiled with the -enable-shared flag. I got the following error during >> the maker install command with both versions: >> >> Configuring MAKER with MPI support >> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >> MPI.c >> /software/mpich/bin/mpicc -c >> -I"/storage/software/intel64/maker-2.27-beta/src" >> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >> MPI.xs: In Funktion ?_MPI_Send?: >> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >> erwartet, aber Argument hat Typ ?int *? >> Running Mkbootstrap for Parallel::Application::MPI () >> chmod 644 MPI.bs >> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >> -fstack-protector MPI.o -o >> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >> \ >> >> /usr/bin/ld: >> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >> making a shared object; recompile with -fPIC >> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >> symbols: Bad value >> collect2: ld gab 1 als Ende-Status zur?ck >> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >> >> A problem was encountered while attempting to compile and install your >> Inline >> C code. The command that failed was: >> make > out.make 2>&1 >> >> The build directory was: >> /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >> ion/MPI >> >> To debug the problem, cd to the build directory, and inspect the output >> files. >> >> at >> /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >> tion/MPI.pm >> line 223 >> >> Does anybody have an idea, what is happening here? >> >> Best regards >> Felix >> >> -- >> Felix Bemm >> Department of Bioinformatics >> University of W?rzburg, Germany >> Tel: +49 931 - 31 83696 >> Fax: +49 931 - 31 84552 >> felix.bemm at uni-wuerzburg.de >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:49:51 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:49:51 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED9271.8090300@uni-wuerzburg.de> Message-ID: I'm Glad it worked. Thanks, Carson On 13-01-09 10:53 AM, "Felix Bemm" wrote: >Thanks Carson, > >version change (to mpich2 1.5) fixed the problem. I did not realize that >I was downloading some mpich3 after all. Thanks again for the fast help! > >Best regards >Felix > >On 09.01.2013 16:18, Carson Holt wrote: >> It is a problem with compilation of the shared libraries in MPICH2. You >> can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS >>and >> CXXFLAGS environmental variables. Alternatively I would recommend not >> using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it >> is the new MPICH3. It is their first attempt to provide full support of >> the new MPI-3 standard, so compared to other MPICH2 releases which all >>use >> the MPI-2 standard it will be very buggy. So avoid it unless your inner >> geek loves the pain that comes from working with bleeding edge advances. >> I would recommend using the last release of MPICH2 which was version >>1.5. >> >> Thanks, >> Carson >> >> >> On 13-01-09 10:09 AM, "Felix Bemm" wrote: >> >>> Hi, >>> >>> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >>> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >>> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >>> compiled with the -enable-shared flag. I got the following error during >>> the maker install command with both versions: >>> >>> Configuring MAKER with MPI support >>> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >>> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv >>>MPI.xsc >>> MPI.c >>> /software/mpich/bin/mpicc -c >>> -I"/storage/software/intel64/maker-2.27-beta/src" >>> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >>> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >>> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >>> MPI.xs: In Funktion ?_MPI_Send?: >>> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >>> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >>> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >>> erwartet, aber Argument hat Typ ?int *? >>> Running Mkbootstrap for Parallel::Application::MPI () >>> chmod 644 MPI.bs >>> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >>> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >>> -fstack-protector MPI.o -o >>> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >>> \ >>> >>> /usr/bin/ld: >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >>> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >>> making a shared object; recompile with -fPIC >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >>> symbols: Bad value >>> collect2: ld gab 1 als Ende-Status zur?ck >>> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >>> >>> A problem was encountered while attempting to compile and install your >>> Inline >>> C code. The command that failed was: >>> make > out.make 2>&1 >>> >>> The build directory was: >>> >>>/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applic >>>at >>> ion/MPI >>> >>> To debug the problem, cd to the build directory, and inspect the output >>> files. >>> >>> at >>> >>>/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Appli >>>ca >>> tion/MPI.pm >>> line 223 >>> >>> Does anybody have an idea, what is happening here? >>> >>> Best regards >>> Felix >>> >>> -- >>> Felix Bemm >>> Department of Bioinformatics >>> University of W?rzburg, Germany >>> Tel: +49 931 - 31 83696 >>> Fax: +49 931 - 31 84552 >>> felix.bemm at uni-wuerzburg.de >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From ranjani at uga.edu Wed Jan 16 09:16:27 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 16 Jan 2013 16:16:27 +0000 Subject: [maker-devel] Transcriptome data to gene models Message-ID: Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Wed Jan 16 10:19:13 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 16 Jan 2013 17:19:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Wed Jan 16 10:24:08 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 16 Jan 2013 17:24:08 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From barry.moore at genetics.utah.edu Wed Jan 16 11:07:57 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 16 Jan 2013 10:07:57 -0800 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> Message-ID: Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Jan 16 11:16:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 16 Jan 2013 13:16:15 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Wed Jan 16 11:26:12 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Wed, 16 Jan 2013 18:26:12 +0000 Subject: [maker-devel] Txome annotation Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA0415B8DE@EXCHANGE-05.internal.solazyme.com> Does anyone have a good suggestion for annotating transcriptomes? In particular calling ORFs (like the best ORF, not just a simple longest ORF) and doing functional annotation? I am currently using cd-hit to try and get a representative transcript set, but I want somthing similar in the ORF space that attempts to call the best, and alternative, ORFs. I am using AutoFact to do functional annotation, and it works, but I don't think it is under continued development. Thanks, Shane ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of maker-devel-request at yandell-lab.org [maker-devel-request at yandell-lab.org] Sent: Wednesday, January 16, 2013 10:16 AM To: maker-devel at yandell-lab.org Subject: maker-devel Digest, Vol 56, Issue 2 Send maker-devel mailing list submissions to maker-devel at yandell-lab.org To subscribe or unsubscribe via the World Wide Web, visit http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org or, via email, send a message with subject or body 'help' to maker-devel-request at yandell-lab.org You can reach the person managing the list at maker-devel-owner at yandell-lab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of maker-devel digest..." Today's Topics: 1. Transcriptome data to gene models (Sivaranjani Namasivayam) 2. Re: Transcriptome data to gene models (Daniel Ence) 3. Re: Transcriptome data to gene models (Fields, Christopher J) 4. Re: Transcriptome data to gene models (Barry Moore) 5. Re: Transcriptome data to gene models (Carson Holt) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Jan 2013 16:16:27 +0000 From: Sivaranjani Namasivayam To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 16 Jan 2013 17:19:13 +0000 From: Daniel Ence To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 16 Jan 2013 17:24:08 +0000 From: "Fields, Christopher J" To: Daniel Ence Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF at CHIMBX5.ad.uillinois.edu> Content-Type: text/plain; charset="iso-8859-1" I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org ------------------------------ Message: 4 Date: Wed, 16 Jan 2013 10:07:57 -0800 From: Barry Moore To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 16 Jan 2013 13:16:15 -0500 From: Carson Holt To: Barry Moore , Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org End of maker-devel Digest, Vol 56, Issue 2 ****************************************** From kapeelc at gmail.com Fri Jan 18 12:00:42 2013 From: kapeelc at gmail.com (Kapeel Chougule) Date: Fri, 18 Jan 2013 12:00:42 -0700 Subject: [maker-devel] BLAST options error Message-ID: Hi, I had this error for one of the chromosomes: BLAST options error: /opt/kapeel/maker_runs/leersia/chr11/Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/comp84263_c0_seq4.for_blastn.fasta does not match input format type, default input type is FASTA ERROR: Failed while collecting blastn reports ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:Chr11 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:Chr11 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/Chr11.286769.311208.0.comp84263_c0_seq4%2Efor_blastn%2Efasta.blastn did not finish on the last run and must be erased Maker is now finished!!! I checked the comp84263_c0_seq4.for_blastn.fasta file for any spaces before > symbol in the header section, it seems to be ok with that. Any suggestions? Thank you, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu From mikael.durling at slu.se Tue Jan 22 02:56:45 2013 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 22 Jan 2013 09:56:45 +0000 Subject: [maker-devel] maker_map_ids anomaly Message-ID: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Hi, I'm trying to load maker annotations into JBrowse, however, the flat file loader can't parse the maker gff stating "parse error: orphans". Looking into one of the broken maker transcripts, it looks like below. Note that the two different mRNAs get the same ID, but a different name. The lines from maker_map_ids are pasted below too. This was a re-annotation run of a previous maker run, which was id_mapped before being used as maker_gff in the current run with model_pass=1 in order to preserve gene names. (btw, loading the unmapped initial maker run into jbrowse works fine.) scf_89829 maker gene 38002 41976 . + . ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; scf_89829 maker mRNA 38002 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=CROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=436|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; scf_89829 maker mRNA 38611 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=maker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33|3|1149|602;_eAED=0.06;Note=Protein of unknown function; scf_89829 maker exon 38002 38349 . + . ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; scf_89829 maker exon 38872 39702 . + . ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 39762 41976 . + . ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 38611 38647 . + . ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38002 38349 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38611 38647 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; Related id map lines: CROS1_G00002820 CROS1_G00002820 maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 CROS1_T00002820_1 CROS1_T00002820_2 and the command line for maker_map_ids: maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ --iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > CrosV1.maker.output/CrosV1.id_map thanks for any hints, Mikael From carsonhh at gmail.com Wed Jan 23 07:42:08 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:42:08 -0700 Subject: [maker-devel] maker_map_ids anomaly In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Message-ID: So does the problem occur immediately following the maker_map_ids step or does it occur after running maker before the maker_map_ids step. I ask so I can identify if it is the maker_map_ids script I neeed to debug or maker. Could you send me the GFF3 file imediatley preceding the step where the error originate. Thanks, Carson On 13-01-22 2:56 AM, "Mikael Brandstr?m Durling" wrote: >Hi, > >I'm trying to load maker annotations into JBrowse, however, the flat file >loader can't parse the maker gff stating "parse error: orphans". Looking >into one of the broken maker transcripts, it looks like below. Note that >the two different mRNAs get the same ID, but a different name. The lines >from maker_map_ids are pasted below too. This was a re-annotation run of >a previous maker run, which was id_mapped before being used as maker_gff >in the current run with model_pass=1 in order to preserve gene names. >(btw, loading the unmapped initial maker run into jbrowse works fine.) > >scf_89829 maker gene 38002 41976 . + . >ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; >scf_89829 maker mRNA 38002 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=C >ROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=4 >36|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; >scf_89829 maker mRNA 38611 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=m >aker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33| >3|1149|602;_eAED=0.06;Note=Protein of unknown function; >scf_89829 maker exon 38002 38349 . + . >ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; >scf_89829 maker exon 38872 39702 . + . >ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 39762 41976 . + . >ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 38611 38647 . + . >ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38002 38349 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38611 38647 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; > > >Related id map lines: > >CROS1_G00002820 CROS1_G00002820 >maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 >CROS1_T00002820_1 CROS1_T00002820_2 > > >and the command line for maker_map_ids: > >maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ >--iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > >CrosV1.maker.output/CrosV1.id_map > >thanks for any hints, >Mikael >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Wed Jan 23 07:59:39 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:59:39 -0700 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Wed Jan 23 08:31:46 2013 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 23 Jan 2013 10:31:46 -0500 Subject: [maker-devel] Question about AED scores Message-ID: Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the *_AED* attribute, which leads to my other question: what does the value of the *_eAED* attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Wed Jan 23 12:42:42 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Wed, 23 Jan 2013 14:42:42 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Message-ID: <51003D32.4080908@jcvi.org> Hello, I'm trying to use the MAKER pipeline to calculate AED scores for the gene models coming out of our annotation pipeline (EVidence Modeler). We then want to compare these computed AED scores with those computed for the gene models coming out of the MAKER2 pipeline. For this purpose, I configured the maker_opts.ctl file like so: 1) Specify gff file coming from our annotation pipeline using `model_gff` param 2) Specify gff file containing est2genome results (computed using MAKER2) using the `est_gff` param 3) Specify gff file containing protein2genome results (computed using MAKER2) using the `protein_gff` param 4) Specify the genome fasta sequence file using the `genome` param I recently configured MAKER 2.27b to work using MPI and I tried launching one contig (chromosome) on a compute node spawning 12 processes like so: mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err Side note: Without MPI, it works fine but takes very very long to complete running on one chromosome (since it is going through the chunks serially). On inspecting the `maker.err` file, I see server error messages that say `DBD::SQLite::db do failed: database is locked`. On referring to a previous email thread on the `maker-devel` mailing list, I see that Carson had replied to the person with a similar issue asking them to check if the working directory and TMP directory are being mounted on an NFS filesystem because this is a potential problem with SQLite databases. Based on that suggestion, I switched the TMP directory to use a local filesytem but the working directory is still NFS mounted. Despite that, I still get this error. The previous email thread had no resolution for this issue. My question is, should the working directory be local as well? I see that despite setting the `TMP` variable, the SQLite DB is getting created in the working directory. What might be the issue? Also, apart from this one error, I notice another error: ERROR: Non-unique top level ID for chr5:hit:1454:4_0 While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. On inspecting the input GFF file (protein2genome), I see that this ID is never repeated. So I have no idea whats going on here either. Any suggestions? Below is my `maker.err` file from the run. (Dropbox link) Thank you very much. Best, Vivek -- Vivek Krishnakumar vkrishnakumar at jcvi.org I've linked 1 file to this email: maker.err (97.7 MB)Dropbox http://db.tt/2tYyKCD7 Mozilla Thunderbird makes it easy to share large files over email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: attachment-24.png Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dropbox.png Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 12:02:12 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 14:02:12 -0500 Subject: [maker-devel] Question about AED scores In-Reply-To: Message-ID: AED from MAKER in the based on nucleotide-level congruency of the transcript compared to the collapsed evidence. eAED is also at the nucleotide level but is adjusted for inferred support of exons, such as can happen with mRNAseq (I.e. I can confirm the splice sites at each end but as the exon gets longer the middle is less likely to be covered). So if I can infer the middle based on ORF and the splice site are confirmed then I consider the middle of the exon to be confirmed for calculating eAED. eAED also adjusts for reading frame from protein evidence alignments, i.e. protein overlap in a different reading frame than the final gene model will not contribute to eAED. So because of this, eAED takes much longer to calculate but is sometimes more useful. Much of the time AED and eAED are identical. Thanks, Carson From: Daniel Standage Date: Wednesday, 23 January, 2013 10:31 AM To: Maker Mailing List Subject: [maker-devel] Question about AED scores Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the _AED attribute, which leads to my other question: what does the value of the _eAED attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Thu Jan 24 12:49:36 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Thu, 24 Jan 2013 14:49:36 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51003D32.4080908@jcvi.org> References: <51003D32.4080908@jcvi.org> Message-ID: <51019050.1030003@jcvi.org> Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the > gene models coming out of our annotation pipeline (EVidence Modeler). > We then want to compare these computed AED scores with those computed > for the gene models coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using > `model_gff` param > 2) Specify gff file containing est2genome results (computed using > MAKER2) using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using > MAKER2) using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried > launching one contig (chromosome) on a compute node spawning 12 > processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to > complete running on one chromosome (since it is going through the > chunks serially). > > On inspecting the `maker.err` file, I see server error messages that > say `DBD::SQLite::db do failed: database is locked`. On referring to a > previous email thread on the `maker-devel` mailing list, I see that > Carson had replied to the person with a similar issue asking them to > check if the working directory and TMP directory are being mounted on > an NFS filesystem because this is a potential problem with SQLite > databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite > that, I still get this error. The previous email thread had no > resolution for this issue. My question is, should the working > directory be local as well? I see that despite setting the `TMP` > variable, the SQLite DB is getting created in the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID > is never repeated. So I have no idea whats going on here either. Any > suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > I've linked 1 file to this email: > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > Mozilla Thunderbird makes it easy to > share large files over email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 13:02:58 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:02:58 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51019050.1030003@jcvi.org> Message-ID: If you still see issue, let me know. I have a hard time seeing how just moving to MPICH2 would have solved the issue. It may also have been an initial problem with the first GFF# db being created and running on a new job recreated it correctly. Either way, let me know if it comes up on your bigger run. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 2:49 PM To: , Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the gene > models coming out of our annotation pipeline (EVidence Modeler). We then want > to compare these computed AED scores with those computed for the gene models > coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using `model_gff` > param > 2) Specify gff file containing est2genome results (computed using MAKER2) > using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using MAKER2) > using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried launching one > contig (chromosome) on a compute node spawning 12 processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to complete > running on one chromosome (since it is going through the chunks serially). > > On inspecting the `maker.err` file, I see server error messages that say > `DBD::SQLite::db do failed: database is locked`. On referring to a previous > email thread on the `maker-devel` mailing list, I see that Carson had replied > to the person with a similar issue asking them to check if the working > directory and TMP directory are being mounted on an NFS filesystem because > this is a potential problem with SQLite databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite that, I > still get this error. The previous email thread had no resolution for this > issue. My question is, should the working directory be local as well? I see > that despite setting the `TMP` variable, the SQLite DB is getting created in > the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID is > never repeated. So I have no idea whats going on here either. Any suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > > > I've linked 1 file to this email: > > > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > > > Mozilla Thunderbird makes it easy to share > large files over email. > > > _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From sbrubaker at solazyme.com Thu Jan 24 13:17:57 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:17:57 +0000 Subject: [maker-devel] Maker-P Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Hi, I heard about Maker-P at PAG. We are working on an algae, which is closer to plants than just about anything else - I am wondering, would Maker-P be useful for us to use instead of regular Maker? From carsonhh at gmail.com Thu Jan 24 13:31:28 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:31:28 -0500 Subject: [maker-devel] FW: Maker-P In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From michael.s.campbell1 at gmail.com Thu Jan 24 13:47:20 2013 From: michael.s.campbell1 at gmail.com (Michael Campbell) Date: Thu, 24 Jan 2013 13:47:20 -0700 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt wrote: > I'm forwarding this to the most relevant people. > > --Carson > > > On 13-01-24 3:17 PM, "Shane Brubaker" wrote: > > >Hi, I heard about Maker-P at PAG. We are working on an algae, which is > >closer to plants than just about anything else - I am wondering, would > >Maker-P be useful for us to use instead of regular Maker? > > > >_______________________________________________ > >maker-devel mailing list > >maker-devel at box290.bluehost.com > >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Thu Jan 24 13:48:19 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:48:19 +0000 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B23517@EXCHANGE-MB01.internal.solazyme.com> Ok that makes sense - Thanks! Sincerely, Shane Brubaker Director of BioInformatics Solazyme, Inc. 225 Gateway Blvd. S. San Francisco, CA 94080 From: Michael Campbell [mailto:michael.s.campbell1 at gmail.com] Sent: Thursday, January 24, 2013 12:47 PM To: Carson Holt Cc: Shane Brubaker; MeiYee Law; Mark Yandell; Maker Mailing List Subject: Re: FW: [maker-devel] Maker-P Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt > wrote: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" > wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 24 14:39:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 16:39:15 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <5101A7D6.4070101@jcvi.org> Message-ID: Done. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 4:29 PM To: Carson Holt Cc: "mcampbell at genetics.utah.edu" Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Ok. Seems to be working fine. I pointed the TMP parameter to our scratch area. Thanks for your suggestion. Should I forward this conversation thread to the maker-devel list ? Vivek On 01/24/2013 04:08 PM, Carson Holt wrote: > > SQLlite will choke almost immediately if it's not set up with the correct > flags, so you will know right away. > > > > > --Carson > > > > > From: "Krishnakumar, Vivek" > Date: Thursday, 24 January, 2013 3:35 PM > To: Carson Holt > Cc: "mcampbell at genetics.utah.edu" > Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked > (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI > > > > > > > Okay. I will try doing that. But how can I find out that my NFS mounted area > has -nolock set? The filesystem areas that we work on are managed by our IT > department. > > Thanks. > Vivek > > > On 01/24/2013 03:27 PM, Carson Holt wrote: > > >> >> If you don't have locally mounted space big enough, then just use an NFS >> mounted /TMP. You will take a slight performance hit, but it may still work >> if it is mounted with -nolock set so SQLite stops complaining. >> >> >> >> >> --Carson >> >> >> >> >> From: "Krishnakumar, Vivek" >> Date: Thursday, 24 January, 2013 3:24 PM >> To: Carson Holt >> Cc: "mcampbell at genetics.utah.edu" >> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >> >> >> >> >> >> >> I no longer see that warning. >> >> The only thing I see is that MAKER now complains that the DB is corrupt, and >> that is because I only have 5GB of /tmp space on the server I currently have >> access to and that is not enough for the whole genome FASTA + est2genome + >> protein2genome + model_gff (EVM). >> >> Thanks, >> Vivek >> >> >> >> On 01/24/2013 03:20 PM, Carson Holt wrote: >> >> >>> >>> You should be able to run on an NFS drive. After creating the initial >>> SQLite database, maker now gives each node it's own copy that is stored in >>> the TMP directory (should be local to each node). Could you send me the >>> GFF3 file that gives the warning, so I can look at it. >>> >>> >>> >>> >>> Thanks, >>> >>> Carson >>> >>> >>> >>> >>> >>> >>> >>> From: "Krishnakumar, Vivek" >>> Date: Thursday, 24 January, 2013 3:17 PM >>> To: Carson Holt >>> Cc: "mcampbell at genetics.utah.edu" >>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>> >>> >>> >>> >>> >>> >>> Hi Carson, >>> >>> I did make sure that every time I reran the pipeline, I deleted the >>> maker.output directory and the temporary files in /tmp. That way I know that >>> the DBs get created fresh. >>> >>> When it was openMPI based, I noticed that irrespective of whether I enabled >>> or disabled the `-TMP` parameter, I would get the database locked error. At >>> this point, mpicc was openMPI based and mpiexec (hydra) was MPICH2 based. >>> >>> On installing MPICH2 as a non-root user and rebuilding `maker`, this issue >>> vanished. Just an observation. >>> >>> The issue I have now with scaling up is that I do not currently have access >>> to a server that has a large amount of non-NFS mounted storage space (we do >>> have such a server but it has been reserved for a different project by a >>> group in our institute). Thus, the creation of the SQLite db is halted mid >>> way and now MAKER complains that the database is corrupt. I can either run >>> the chromosomes individually (serially) and then the scaffolds as one group >>> or wait to get a time slot of that server. >>> >>> Will let you know if I have any more issues. >>> >>> Thank you. >>> Vivek >>> >>> >>> >>> On 01/24/2013 03:02 PM, Carson Holt wrote: >>> >>> >>>> >>>> If you still see issue, let me know. I have a hard time seeing how just >>>> moving to MPICH2 would have solved the issue. It may also have been an >>>> initial problem with the first GFF# db being created and running on a new >>>> job recreated it correctly. Either way, let me know if it comes up on your >>>> bigger run. >>>> >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Carson >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> From: "Krishnakumar, Vivek" >>>> Date: Thursday, 24 January, 2013 2:49 PM >>>> To: , >>>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>>> >>>> >>>> >>>> >>>> >>>> >>>> Hi Everybody, >>>> >>>> Sorry for jumping the gun and writing to the mailing list before >>>> completely troubleshooting this issue. I was able to figure out the problem >>>> and get MAKER 2.27b working fine in MPI mode. >>>> >>>> The issue was with the incorrect version of mpicc (it was openMPI based >>>> and not mpich2). I was able to successfully run through the steps described >>>> below on one chromosome in under a few hours (~2). Now I'm scaling it to >>>> the whole genome (8 chromosomes and ~2200 unanchored scaffolds). >>>> >>>> Thank you. >>>> Vivek >>>> >>>> >>>> On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I'm trying to use the MAKER pipeline to calculate AED scores for the gene >>>>> models coming out of our annotation pipeline (EVidence Modeler). We then >>>>> want to compare these computed AED scores with those computed for the gene >>>>> models coming out of the MAKER2 pipeline. >>>>> >>>>> For this purpose, I configured the maker_opts.ctl file like so: >>>>> 1) Specify gff file coming from our annotation pipeline using `model_gff` >>>>> param >>>>> 2) Specify gff file containing est2genome results (computed using MAKER2) >>>>> using the `est_gff` param >>>>> 3) Specify gff file containing protein2genome results (computed using >>>>> MAKER2) using the `protein_gff` param >>>>> 4) Specify the genome fasta sequence file using the `genome` param >>>>> >>>>> I recently configured MAKER 2.27b to work using MPI and I tried launching >>>>> one contig (chromosome) on a compute node spawning 12 processes like so: >>>>> mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl >>>>> maker_exe.ctl 2>&1 | tee maker.err >>>>> >>>>> Side note: Without MPI, it works fine but takes very very long to >>>>> complete running on one chromosome (since it is going through the chunks >>>>> serially). >>>>> >>>>> On inspecting the `maker.err` file, I see server error messages that say >>>>> `DBD::SQLite::db do failed: database is locked`. On referring to a >>>>> previous email thread on the `maker-devel` mailing list, I see that Carson >>>>> had replied to the person with a similar issue asking them to check if the >>>>> working directory and TMP directory are being mounted on an NFS filesystem >>>>> because this is a potential problem with SQLite databases. >>>>> >>>>> Based on that suggestion, I switched the TMP directory to use a local >>>>> filesytem but the working directory is still NFS mounted. Despite that, I >>>>> still get this error. The previous email thread had no resolution for this >>>>> issue. My question is, should the working directory be local as well? I >>>>> see that despite setting the `TMP` variable, the SQLite DB is getting >>>>> created in the working directory. >>>>> >>>>> What might be the issue? >>>>> >>>>> Also, apart from this one error, I notice another error: >>>>> ERROR: Non-unique top level ID for chr5:hit:1454:4_0 >>>>> While this is technically legal in GFF3, it usually >>>>> indicates a poorly fomatted GFF3 file (perhaps you >>>>> tried to merge two GFF3 files without accounting for >>>>> unique IDs). MAKER will not handle these correctly. >>>>> >>>>> On inspecting the input GFF file (protein2genome), I see that this ID is >>>>> never repeated. So I have no idea whats going on here either. Any >>>>> suggestions? >>>>> >>>>> Below is my `maker.err` file from the run. (Dropbox link) >>>>> >>>>> Thank you very much. >>>>> Best, >>>>> >>>>> Vivek >>>>> >>>>> -- >>>>> Vivek Krishnakumar >>>>> vkrishnakumar at jcvi.org >>>>> >>>>> >>>>> >>>>> I've linked 1 file to this email: >>>>> >>>>> >>>>> maker.err (97.7 MB)Dropbox >>>>> http://db.tt/2tYyKCD7 >>>>> >>>>> >>>>> Mozilla Thunderbird makes it easy to >>>>> share large files over email. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> _______________________________________________ maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >>> >> >> >> >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From ranjani at uga.edu Thu Jan 24 22:17:13 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Fri, 25 Jan 2013 05:17:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: , Message-ID: I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam > Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" > Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 11:43:17 2013 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2013 13:43:17 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Also since single exon ESTs are almost always coming from background transcription and not real genes, MAKER may also require some sort of protein alignment or ab initio predictor support before promoting them to gene models. --Carson From: Sivaranjani Namasivayam Date: Friday, 25 January, 2013 12:17 AM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] Transcriptome data to gene models I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Tue Jan 29 09:50:24 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 29 Jan 2013 09:50:24 -0700 Subject: [maker-devel] Fwd: Help in installation of MAKER2 References: Message-ID: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 09:57:25 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 11:57:25 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: If it is a 64 bit Intel Mac make sure you install the 64 bit version of fink and not the 32 bit version. Then use fink to install both of these --> glib2-dev glib2-shlibs Installing them any other way on a Mac makes it so much harder to get the configuration right. Do 'fink remove' if you've already installed them with fink, then update fink and make sure it is the right fink for your processor before reinstalling. --Carson From: Barry Moore Date: Tuesday, 29 January, 2013 11:50 AM To: Maker Mailing List Cc: Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Jan 29 09:58:57 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 29 Jan 2013 16:58:57 +0000 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> References: , <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 Date: January 29, 2013 4:45:49 AM MST To: > Hi Barry, I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: checking for socklen_t... yes checking for pkg-config... no ERROR: Could not find pkg-config ... is glib-2 installed ??? macpro:exonerate-2.2.0 admin$ pkg-get -bash: pkg-get: command not found I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 10:04:54 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 12:04:54 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: Message-ID: I had problems moving from OS X 10.5 to 10.6 and from 10.6 to 10.7. All of which were solved by reinstalling fink (for the right processor ? 32bit vs 64bit) and all tools and libraries I had from fink. Thanks, Carson From: Daniel Ence Date: Tuesday, 29 January, 2013 11:58 AM To: Maker Mailing List , Carson Holt Cc: "alexmendozasoler at gmail.com" Subject: RE: [maker-devel] Fwd: Help in installation of MAKER2 Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:09:23 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:09:23 +0100 Subject: [maker-devel] Compilation Problems Message-ID: <50ED8823.8050001@uni-wuerzburg.de> Hi, I am trying to compile maker (2.27-beta) with MPI support on Ubuntu 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and a self compiled version (MPICH2 3.0.1) at hand. The latter one was compiled with the -enable-shared flag. I got the following error during the maker install command with both versions: Configuring MAKER with MPI support /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc MPI.c /software/mpich/bin/mpicc -c -I"/storage/software/intel64/maker-2.27-beta/src" -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c MPI.xs: In Funktion ?_MPI_Send?: MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? von inkompatiblem Zeigertyp [standardm??ig aktiviert] /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? erwartet, aber Argument hat Typ ?int *? Running Mkbootstrap for Parallel::Application::MPI () chmod 644 MPI.bs rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib -fstack-protector MPI.o -o blib/arch/auto/Parallel/Application/MPI/MPI.so \ \ /usr/bin/ld: /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when making a shared object; recompile with -fPIC /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read symbols: Bad value collect2: ld gab 1 als Ende-Status zur?ck make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make > out.make 2>&1 The build directory was: /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Application/MPI To debug the problem, cd to the build directory, and inspect the output files. at /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Application/MPI.pm line 223 Does anybody have an idea, what is happening here? Best regards Felix -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:18:06 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:18:06 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED8823.8050001@uni-wuerzburg.de> Message-ID: It is a problem with compilation of the shared libraries in MPICH2. You can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and CXXFLAGS environmental variables. Alternatively I would recommend not using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it is the new MPICH3. It is their first attempt to provide full support of the new MPI-3 standard, so compared to other MPICH2 releases which all use the MPI-2 standard it will be very buggy. So avoid it unless your inner geek loves the pain that comes from working with bleeding edge advances. I would recommend using the last release of MPICH2 which was version 1.5. Thanks, Carson On 13-01-09 10:09 AM, "Felix Bemm" wrote: >Hi, > >I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >a self compiled version (MPICH2 3.0.1) at hand. The latter one was >compiled with the -enable-shared flag. I got the following error during >the maker install command with both versions: > >Configuring MAKER with MPI support >/usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >"/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >MPI.c >/software/mpich/bin/mpicc -c >-I"/storage/software/intel64/maker-2.27-beta/src" >-I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >MPI.xs: In Funktion ?_MPI_Send?: >MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >von inkompatiblem Zeigertyp [standardm??ig aktiviert] >/usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >erwartet, aber Argument hat Typ ?int *? >Running Mkbootstrap for Parallel::Application::MPI () >chmod 644 MPI.bs >rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >/software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >-fstack-protector MPI.o -o >blib/arch/auto/Parallel/Application/MPI/MPI.so \ > \ > >/usr/bin/ld: >/storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >making a shared object; recompile with -fPIC >/storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >symbols: Bad value >collect2: ld gab 1 als Ende-Status zur?ck >make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 > >A problem was encountered while attempting to compile and install your >Inline >C code. The command that failed was: > make > out.make 2>&1 > >The build directory was: >/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >ion/MPI > >To debug the problem, cd to the build directory, and inspect the output >files. > > at >/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >tion/MPI.pm >line 223 > >Does anybody have an idea, what is happening here? > >Best regards >Felix > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:53:21 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:53:21 +0100 Subject: [maker-devel] Compilation Problems In-Reply-To: References: Message-ID: <50ED9271.8090300@uni-wuerzburg.de> Thanks Carson, version change (to mpich2 1.5) fixed the problem. I did not realize that I was downloading some mpich3 after all. Thanks again for the fast help! Best regards Felix On 09.01.2013 16:18, Carson Holt wrote: > It is a problem with compilation of the shared libraries in MPICH2. You > can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and > CXXFLAGS environmental variables. Alternatively I would recommend not > using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it > is the new MPICH3. It is their first attempt to provide full support of > the new MPI-3 standard, so compared to other MPICH2 releases which all use > the MPI-2 standard it will be very buggy. So avoid it unless your inner > geek loves the pain that comes from working with bleeding edge advances. > I would recommend using the last release of MPICH2 which was version 1.5. > > Thanks, > Carson > > > On 13-01-09 10:09 AM, "Felix Bemm" wrote: > >> Hi, >> >> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >> compiled with the -enable-shared flag. I got the following error during >> the maker install command with both versions: >> >> Configuring MAKER with MPI support >> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >> MPI.c >> /software/mpich/bin/mpicc -c >> -I"/storage/software/intel64/maker-2.27-beta/src" >> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >> MPI.xs: In Funktion ?_MPI_Send?: >> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >> erwartet, aber Argument hat Typ ?int *? >> Running Mkbootstrap for Parallel::Application::MPI () >> chmod 644 MPI.bs >> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >> -fstack-protector MPI.o -o >> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >> \ >> >> /usr/bin/ld: >> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >> making a shared object; recompile with -fPIC >> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >> symbols: Bad value >> collect2: ld gab 1 als Ende-Status zur?ck >> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >> >> A problem was encountered while attempting to compile and install your >> Inline >> C code. The command that failed was: >> make > out.make 2>&1 >> >> The build directory was: >> /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >> ion/MPI >> >> To debug the problem, cd to the build directory, and inspect the output >> files. >> >> at >> /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >> tion/MPI.pm >> line 223 >> >> Does anybody have an idea, what is happening here? >> >> Best regards >> Felix >> >> -- >> Felix Bemm >> Department of Bioinformatics >> University of W?rzburg, Germany >> Tel: +49 931 - 31 83696 >> Fax: +49 931 - 31 84552 >> felix.bemm at uni-wuerzburg.de >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:49:51 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:49:51 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED9271.8090300@uni-wuerzburg.de> Message-ID: I'm Glad it worked. Thanks, Carson On 13-01-09 10:53 AM, "Felix Bemm" wrote: >Thanks Carson, > >version change (to mpich2 1.5) fixed the problem. I did not realize that >I was downloading some mpich3 after all. Thanks again for the fast help! > >Best regards >Felix > >On 09.01.2013 16:18, Carson Holt wrote: >> It is a problem with compilation of the shared libraries in MPICH2. You >> can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS >>and >> CXXFLAGS environmental variables. Alternatively I would recommend not >> using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it >> is the new MPICH3. It is their first attempt to provide full support of >> the new MPI-3 standard, so compared to other MPICH2 releases which all >>use >> the MPI-2 standard it will be very buggy. So avoid it unless your inner >> geek loves the pain that comes from working with bleeding edge advances. >> I would recommend using the last release of MPICH2 which was version >>1.5. >> >> Thanks, >> Carson >> >> >> On 13-01-09 10:09 AM, "Felix Bemm" wrote: >> >>> Hi, >>> >>> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >>> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >>> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >>> compiled with the -enable-shared flag. I got the following error during >>> the maker install command with both versions: >>> >>> Configuring MAKER with MPI support >>> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >>> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv >>>MPI.xsc >>> MPI.c >>> /software/mpich/bin/mpicc -c >>> -I"/storage/software/intel64/maker-2.27-beta/src" >>> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >>> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >>> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >>> MPI.xs: In Funktion ?_MPI_Send?: >>> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >>> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >>> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >>> erwartet, aber Argument hat Typ ?int *? >>> Running Mkbootstrap for Parallel::Application::MPI () >>> chmod 644 MPI.bs >>> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >>> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >>> -fstack-protector MPI.o -o >>> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >>> \ >>> >>> /usr/bin/ld: >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >>> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >>> making a shared object; recompile with -fPIC >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >>> symbols: Bad value >>> collect2: ld gab 1 als Ende-Status zur?ck >>> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >>> >>> A problem was encountered while attempting to compile and install your >>> Inline >>> C code. The command that failed was: >>> make > out.make 2>&1 >>> >>> The build directory was: >>> >>>/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applic >>>at >>> ion/MPI >>> >>> To debug the problem, cd to the build directory, and inspect the output >>> files. >>> >>> at >>> >>>/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Appli >>>ca >>> tion/MPI.pm >>> line 223 >>> >>> Does anybody have an idea, what is happening here? >>> >>> Best regards >>> Felix >>> >>> -- >>> Felix Bemm >>> Department of Bioinformatics >>> University of W?rzburg, Germany >>> Tel: +49 931 - 31 83696 >>> Fax: +49 931 - 31 84552 >>> felix.bemm at uni-wuerzburg.de >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From ranjani at uga.edu Wed Jan 16 09:16:27 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 16 Jan 2013 16:16:27 +0000 Subject: [maker-devel] Transcriptome data to gene models Message-ID: Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Wed Jan 16 10:19:13 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 16 Jan 2013 17:19:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Wed Jan 16 10:24:08 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 16 Jan 2013 17:24:08 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From barry.moore at genetics.utah.edu Wed Jan 16 11:07:57 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 16 Jan 2013 10:07:57 -0800 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> Message-ID: Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Jan 16 11:16:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 16 Jan 2013 13:16:15 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Wed Jan 16 11:26:12 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Wed, 16 Jan 2013 18:26:12 +0000 Subject: [maker-devel] Txome annotation Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA0415B8DE@EXCHANGE-05.internal.solazyme.com> Does anyone have a good suggestion for annotating transcriptomes? In particular calling ORFs (like the best ORF, not just a simple longest ORF) and doing functional annotation? I am currently using cd-hit to try and get a representative transcript set, but I want somthing similar in the ORF space that attempts to call the best, and alternative, ORFs. I am using AutoFact to do functional annotation, and it works, but I don't think it is under continued development. Thanks, Shane ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of maker-devel-request at yandell-lab.org [maker-devel-request at yandell-lab.org] Sent: Wednesday, January 16, 2013 10:16 AM To: maker-devel at yandell-lab.org Subject: maker-devel Digest, Vol 56, Issue 2 Send maker-devel mailing list submissions to maker-devel at yandell-lab.org To subscribe or unsubscribe via the World Wide Web, visit http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org or, via email, send a message with subject or body 'help' to maker-devel-request at yandell-lab.org You can reach the person managing the list at maker-devel-owner at yandell-lab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of maker-devel digest..." Today's Topics: 1. Transcriptome data to gene models (Sivaranjani Namasivayam) 2. Re: Transcriptome data to gene models (Daniel Ence) 3. Re: Transcriptome data to gene models (Fields, Christopher J) 4. Re: Transcriptome data to gene models (Barry Moore) 5. Re: Transcriptome data to gene models (Carson Holt) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Jan 2013 16:16:27 +0000 From: Sivaranjani Namasivayam To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 16 Jan 2013 17:19:13 +0000 From: Daniel Ence To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 16 Jan 2013 17:24:08 +0000 From: "Fields, Christopher J" To: Daniel Ence Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF at CHIMBX5.ad.uillinois.edu> Content-Type: text/plain; charset="iso-8859-1" I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org ------------------------------ Message: 4 Date: Wed, 16 Jan 2013 10:07:57 -0800 From: Barry Moore To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 16 Jan 2013 13:16:15 -0500 From: Carson Holt To: Barry Moore , Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org End of maker-devel Digest, Vol 56, Issue 2 ****************************************** From kapeelc at gmail.com Fri Jan 18 12:00:42 2013 From: kapeelc at gmail.com (Kapeel Chougule) Date: Fri, 18 Jan 2013 12:00:42 -0700 Subject: [maker-devel] BLAST options error Message-ID: Hi, I had this error for one of the chromosomes: BLAST options error: /opt/kapeel/maker_runs/leersia/chr11/Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/comp84263_c0_seq4.for_blastn.fasta does not match input format type, default input type is FASTA ERROR: Failed while collecting blastn reports ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:Chr11 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:Chr11 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/Chr11.286769.311208.0.comp84263_c0_seq4%2Efor_blastn%2Efasta.blastn did not finish on the last run and must be erased Maker is now finished!!! I checked the comp84263_c0_seq4.for_blastn.fasta file for any spaces before > symbol in the header section, it seems to be ok with that. Any suggestions? Thank you, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu From mikael.durling at slu.se Tue Jan 22 02:56:45 2013 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 22 Jan 2013 09:56:45 +0000 Subject: [maker-devel] maker_map_ids anomaly Message-ID: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Hi, I'm trying to load maker annotations into JBrowse, however, the flat file loader can't parse the maker gff stating "parse error: orphans". Looking into one of the broken maker transcripts, it looks like below. Note that the two different mRNAs get the same ID, but a different name. The lines from maker_map_ids are pasted below too. This was a re-annotation run of a previous maker run, which was id_mapped before being used as maker_gff in the current run with model_pass=1 in order to preserve gene names. (btw, loading the unmapped initial maker run into jbrowse works fine.) scf_89829 maker gene 38002 41976 . + . ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; scf_89829 maker mRNA 38002 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=CROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=436|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; scf_89829 maker mRNA 38611 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=maker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33|3|1149|602;_eAED=0.06;Note=Protein of unknown function; scf_89829 maker exon 38002 38349 . + . ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; scf_89829 maker exon 38872 39702 . + . ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 39762 41976 . + . ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 38611 38647 . + . ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38002 38349 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38611 38647 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; Related id map lines: CROS1_G00002820 CROS1_G00002820 maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 CROS1_T00002820_1 CROS1_T00002820_2 and the command line for maker_map_ids: maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ --iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > CrosV1.maker.output/CrosV1.id_map thanks for any hints, Mikael From carsonhh at gmail.com Wed Jan 23 07:42:08 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:42:08 -0700 Subject: [maker-devel] maker_map_ids anomaly In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Message-ID: So does the problem occur immediately following the maker_map_ids step or does it occur after running maker before the maker_map_ids step. I ask so I can identify if it is the maker_map_ids script I neeed to debug or maker. Could you send me the GFF3 file imediatley preceding the step where the error originate. Thanks, Carson On 13-01-22 2:56 AM, "Mikael Brandstr?m Durling" wrote: >Hi, > >I'm trying to load maker annotations into JBrowse, however, the flat file >loader can't parse the maker gff stating "parse error: orphans". Looking >into one of the broken maker transcripts, it looks like below. Note that >the two different mRNAs get the same ID, but a different name. The lines >from maker_map_ids are pasted below too. This was a re-annotation run of >a previous maker run, which was id_mapped before being used as maker_gff >in the current run with model_pass=1 in order to preserve gene names. >(btw, loading the unmapped initial maker run into jbrowse works fine.) > >scf_89829 maker gene 38002 41976 . + . >ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; >scf_89829 maker mRNA 38002 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=C >ROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=4 >36|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; >scf_89829 maker mRNA 38611 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=m >aker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33| >3|1149|602;_eAED=0.06;Note=Protein of unknown function; >scf_89829 maker exon 38002 38349 . + . >ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; >scf_89829 maker exon 38872 39702 . + . >ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 39762 41976 . + . >ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 38611 38647 . + . >ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38002 38349 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38611 38647 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; > > >Related id map lines: > >CROS1_G00002820 CROS1_G00002820 >maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 >CROS1_T00002820_1 CROS1_T00002820_2 > > >and the command line for maker_map_ids: > >maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ >--iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > >CrosV1.maker.output/CrosV1.id_map > >thanks for any hints, >Mikael >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Wed Jan 23 07:59:39 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:59:39 -0700 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Wed Jan 23 08:31:46 2013 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 23 Jan 2013 10:31:46 -0500 Subject: [maker-devel] Question about AED scores Message-ID: Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the *_AED* attribute, which leads to my other question: what does the value of the *_eAED* attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Wed Jan 23 12:42:42 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Wed, 23 Jan 2013 14:42:42 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Message-ID: <51003D32.4080908@jcvi.org> Hello, I'm trying to use the MAKER pipeline to calculate AED scores for the gene models coming out of our annotation pipeline (EVidence Modeler). We then want to compare these computed AED scores with those computed for the gene models coming out of the MAKER2 pipeline. For this purpose, I configured the maker_opts.ctl file like so: 1) Specify gff file coming from our annotation pipeline using `model_gff` param 2) Specify gff file containing est2genome results (computed using MAKER2) using the `est_gff` param 3) Specify gff file containing protein2genome results (computed using MAKER2) using the `protein_gff` param 4) Specify the genome fasta sequence file using the `genome` param I recently configured MAKER 2.27b to work using MPI and I tried launching one contig (chromosome) on a compute node spawning 12 processes like so: mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err Side note: Without MPI, it works fine but takes very very long to complete running on one chromosome (since it is going through the chunks serially). On inspecting the `maker.err` file, I see server error messages that say `DBD::SQLite::db do failed: database is locked`. On referring to a previous email thread on the `maker-devel` mailing list, I see that Carson had replied to the person with a similar issue asking them to check if the working directory and TMP directory are being mounted on an NFS filesystem because this is a potential problem with SQLite databases. Based on that suggestion, I switched the TMP directory to use a local filesytem but the working directory is still NFS mounted. Despite that, I still get this error. The previous email thread had no resolution for this issue. My question is, should the working directory be local as well? I see that despite setting the `TMP` variable, the SQLite DB is getting created in the working directory. What might be the issue? Also, apart from this one error, I notice another error: ERROR: Non-unique top level ID for chr5:hit:1454:4_0 While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. On inspecting the input GFF file (protein2genome), I see that this ID is never repeated. So I have no idea whats going on here either. Any suggestions? Below is my `maker.err` file from the run. (Dropbox link) Thank you very much. Best, Vivek -- Vivek Krishnakumar vkrishnakumar at jcvi.org I've linked 1 file to this email: maker.err (97.7 MB)Dropbox http://db.tt/2tYyKCD7 Mozilla Thunderbird makes it easy to share large files over email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: attachment-24.png Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dropbox.png Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 12:02:12 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 14:02:12 -0500 Subject: [maker-devel] Question about AED scores In-Reply-To: Message-ID: AED from MAKER in the based on nucleotide-level congruency of the transcript compared to the collapsed evidence. eAED is also at the nucleotide level but is adjusted for inferred support of exons, such as can happen with mRNAseq (I.e. I can confirm the splice sites at each end but as the exon gets longer the middle is less likely to be covered). So if I can infer the middle based on ORF and the splice site are confirmed then I consider the middle of the exon to be confirmed for calculating eAED. eAED also adjusts for reading frame from protein evidence alignments, i.e. protein overlap in a different reading frame than the final gene model will not contribute to eAED. So because of this, eAED takes much longer to calculate but is sometimes more useful. Much of the time AED and eAED are identical. Thanks, Carson From: Daniel Standage Date: Wednesday, 23 January, 2013 10:31 AM To: Maker Mailing List Subject: [maker-devel] Question about AED scores Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the _AED attribute, which leads to my other question: what does the value of the _eAED attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Thu Jan 24 12:49:36 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Thu, 24 Jan 2013 14:49:36 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51003D32.4080908@jcvi.org> References: <51003D32.4080908@jcvi.org> Message-ID: <51019050.1030003@jcvi.org> Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the > gene models coming out of our annotation pipeline (EVidence Modeler). > We then want to compare these computed AED scores with those computed > for the gene models coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using > `model_gff` param > 2) Specify gff file containing est2genome results (computed using > MAKER2) using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using > MAKER2) using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried > launching one contig (chromosome) on a compute node spawning 12 > processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to > complete running on one chromosome (since it is going through the > chunks serially). > > On inspecting the `maker.err` file, I see server error messages that > say `DBD::SQLite::db do failed: database is locked`. On referring to a > previous email thread on the `maker-devel` mailing list, I see that > Carson had replied to the person with a similar issue asking them to > check if the working directory and TMP directory are being mounted on > an NFS filesystem because this is a potential problem with SQLite > databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite > that, I still get this error. The previous email thread had no > resolution for this issue. My question is, should the working > directory be local as well? I see that despite setting the `TMP` > variable, the SQLite DB is getting created in the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID > is never repeated. So I have no idea whats going on here either. Any > suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > I've linked 1 file to this email: > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > Mozilla Thunderbird makes it easy to > share large files over email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 13:02:58 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:02:58 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51019050.1030003@jcvi.org> Message-ID: If you still see issue, let me know. I have a hard time seeing how just moving to MPICH2 would have solved the issue. It may also have been an initial problem with the first GFF# db being created and running on a new job recreated it correctly. Either way, let me know if it comes up on your bigger run. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 2:49 PM To: , Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the gene > models coming out of our annotation pipeline (EVidence Modeler). We then want > to compare these computed AED scores with those computed for the gene models > coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using `model_gff` > param > 2) Specify gff file containing est2genome results (computed using MAKER2) > using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using MAKER2) > using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried launching one > contig (chromosome) on a compute node spawning 12 processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to complete > running on one chromosome (since it is going through the chunks serially). > > On inspecting the `maker.err` file, I see server error messages that say > `DBD::SQLite::db do failed: database is locked`. On referring to a previous > email thread on the `maker-devel` mailing list, I see that Carson had replied > to the person with a similar issue asking them to check if the working > directory and TMP directory are being mounted on an NFS filesystem because > this is a potential problem with SQLite databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite that, I > still get this error. The previous email thread had no resolution for this > issue. My question is, should the working directory be local as well? I see > that despite setting the `TMP` variable, the SQLite DB is getting created in > the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID is > never repeated. So I have no idea whats going on here either. Any suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > > > I've linked 1 file to this email: > > > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > > > Mozilla Thunderbird makes it easy to share > large files over email. > > > _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From sbrubaker at solazyme.com Thu Jan 24 13:17:57 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:17:57 +0000 Subject: [maker-devel] Maker-P Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Hi, I heard about Maker-P at PAG. We are working on an algae, which is closer to plants than just about anything else - I am wondering, would Maker-P be useful for us to use instead of regular Maker? From carsonhh at gmail.com Thu Jan 24 13:31:28 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:31:28 -0500 Subject: [maker-devel] FW: Maker-P In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From michael.s.campbell1 at gmail.com Thu Jan 24 13:47:20 2013 From: michael.s.campbell1 at gmail.com (Michael Campbell) Date: Thu, 24 Jan 2013 13:47:20 -0700 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt wrote: > I'm forwarding this to the most relevant people. > > --Carson > > > On 13-01-24 3:17 PM, "Shane Brubaker" wrote: > > >Hi, I heard about Maker-P at PAG. We are working on an algae, which is > >closer to plants than just about anything else - I am wondering, would > >Maker-P be useful for us to use instead of regular Maker? > > > >_______________________________________________ > >maker-devel mailing list > >maker-devel at box290.bluehost.com > >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Thu Jan 24 13:48:19 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:48:19 +0000 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B23517@EXCHANGE-MB01.internal.solazyme.com> Ok that makes sense - Thanks! Sincerely, Shane Brubaker Director of BioInformatics Solazyme, Inc. 225 Gateway Blvd. S. San Francisco, CA 94080 From: Michael Campbell [mailto:michael.s.campbell1 at gmail.com] Sent: Thursday, January 24, 2013 12:47 PM To: Carson Holt Cc: Shane Brubaker; MeiYee Law; Mark Yandell; Maker Mailing List Subject: Re: FW: [maker-devel] Maker-P Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt > wrote: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" > wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 24 14:39:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 16:39:15 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <5101A7D6.4070101@jcvi.org> Message-ID: Done. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 4:29 PM To: Carson Holt Cc: "mcampbell at genetics.utah.edu" Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Ok. Seems to be working fine. I pointed the TMP parameter to our scratch area. Thanks for your suggestion. Should I forward this conversation thread to the maker-devel list ? Vivek On 01/24/2013 04:08 PM, Carson Holt wrote: > > SQLlite will choke almost immediately if it's not set up with the correct > flags, so you will know right away. > > > > > --Carson > > > > > From: "Krishnakumar, Vivek" > Date: Thursday, 24 January, 2013 3:35 PM > To: Carson Holt > Cc: "mcampbell at genetics.utah.edu" > Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked > (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI > > > > > > > Okay. I will try doing that. But how can I find out that my NFS mounted area > has -nolock set? The filesystem areas that we work on are managed by our IT > department. > > Thanks. > Vivek > > > On 01/24/2013 03:27 PM, Carson Holt wrote: > > >> >> If you don't have locally mounted space big enough, then just use an NFS >> mounted /TMP. You will take a slight performance hit, but it may still work >> if it is mounted with -nolock set so SQLite stops complaining. >> >> >> >> >> --Carson >> >> >> >> >> From: "Krishnakumar, Vivek" >> Date: Thursday, 24 January, 2013 3:24 PM >> To: Carson Holt >> Cc: "mcampbell at genetics.utah.edu" >> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >> >> >> >> >> >> >> I no longer see that warning. >> >> The only thing I see is that MAKER now complains that the DB is corrupt, and >> that is because I only have 5GB of /tmp space on the server I currently have >> access to and that is not enough for the whole genome FASTA + est2genome + >> protein2genome + model_gff (EVM). >> >> Thanks, >> Vivek >> >> >> >> On 01/24/2013 03:20 PM, Carson Holt wrote: >> >> >>> >>> You should be able to run on an NFS drive. After creating the initial >>> SQLite database, maker now gives each node it's own copy that is stored in >>> the TMP directory (should be local to each node). Could you send me the >>> GFF3 file that gives the warning, so I can look at it. >>> >>> >>> >>> >>> Thanks, >>> >>> Carson >>> >>> >>> >>> >>> >>> >>> >>> From: "Krishnakumar, Vivek" >>> Date: Thursday, 24 January, 2013 3:17 PM >>> To: Carson Holt >>> Cc: "mcampbell at genetics.utah.edu" >>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>> >>> >>> >>> >>> >>> >>> Hi Carson, >>> >>> I did make sure that every time I reran the pipeline, I deleted the >>> maker.output directory and the temporary files in /tmp. That way I know that >>> the DBs get created fresh. >>> >>> When it was openMPI based, I noticed that irrespective of whether I enabled >>> or disabled the `-TMP` parameter, I would get the database locked error. At >>> this point, mpicc was openMPI based and mpiexec (hydra) was MPICH2 based. >>> >>> On installing MPICH2 as a non-root user and rebuilding `maker`, this issue >>> vanished. Just an observation. >>> >>> The issue I have now with scaling up is that I do not currently have access >>> to a server that has a large amount of non-NFS mounted storage space (we do >>> have such a server but it has been reserved for a different project by a >>> group in our institute). Thus, the creation of the SQLite db is halted mid >>> way and now MAKER complains that the database is corrupt. I can either run >>> the chromosomes individually (serially) and then the scaffolds as one group >>> or wait to get a time slot of that server. >>> >>> Will let you know if I have any more issues. >>> >>> Thank you. >>> Vivek >>> >>> >>> >>> On 01/24/2013 03:02 PM, Carson Holt wrote: >>> >>> >>>> >>>> If you still see issue, let me know. I have a hard time seeing how just >>>> moving to MPICH2 would have solved the issue. It may also have been an >>>> initial problem with the first GFF# db being created and running on a new >>>> job recreated it correctly. Either way, let me know if it comes up on your >>>> bigger run. >>>> >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Carson >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> From: "Krishnakumar, Vivek" >>>> Date: Thursday, 24 January, 2013 2:49 PM >>>> To: , >>>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>>> >>>> >>>> >>>> >>>> >>>> >>>> Hi Everybody, >>>> >>>> Sorry for jumping the gun and writing to the mailing list before >>>> completely troubleshooting this issue. I was able to figure out the problem >>>> and get MAKER 2.27b working fine in MPI mode. >>>> >>>> The issue was with the incorrect version of mpicc (it was openMPI based >>>> and not mpich2). I was able to successfully run through the steps described >>>> below on one chromosome in under a few hours (~2). Now I'm scaling it to >>>> the whole genome (8 chromosomes and ~2200 unanchored scaffolds). >>>> >>>> Thank you. >>>> Vivek >>>> >>>> >>>> On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I'm trying to use the MAKER pipeline to calculate AED scores for the gene >>>>> models coming out of our annotation pipeline (EVidence Modeler). We then >>>>> want to compare these computed AED scores with those computed for the gene >>>>> models coming out of the MAKER2 pipeline. >>>>> >>>>> For this purpose, I configured the maker_opts.ctl file like so: >>>>> 1) Specify gff file coming from our annotation pipeline using `model_gff` >>>>> param >>>>> 2) Specify gff file containing est2genome results (computed using MAKER2) >>>>> using the `est_gff` param >>>>> 3) Specify gff file containing protein2genome results (computed using >>>>> MAKER2) using the `protein_gff` param >>>>> 4) Specify the genome fasta sequence file using the `genome` param >>>>> >>>>> I recently configured MAKER 2.27b to work using MPI and I tried launching >>>>> one contig (chromosome) on a compute node spawning 12 processes like so: >>>>> mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl >>>>> maker_exe.ctl 2>&1 | tee maker.err >>>>> >>>>> Side note: Without MPI, it works fine but takes very very long to >>>>> complete running on one chromosome (since it is going through the chunks >>>>> serially). >>>>> >>>>> On inspecting the `maker.err` file, I see server error messages that say >>>>> `DBD::SQLite::db do failed: database is locked`. On referring to a >>>>> previous email thread on the `maker-devel` mailing list, I see that Carson >>>>> had replied to the person with a similar issue asking them to check if the >>>>> working directory and TMP directory are being mounted on an NFS filesystem >>>>> because this is a potential problem with SQLite databases. >>>>> >>>>> Based on that suggestion, I switched the TMP directory to use a local >>>>> filesytem but the working directory is still NFS mounted. Despite that, I >>>>> still get this error. The previous email thread had no resolution for this >>>>> issue. My question is, should the working directory be local as well? I >>>>> see that despite setting the `TMP` variable, the SQLite DB is getting >>>>> created in the working directory. >>>>> >>>>> What might be the issue? >>>>> >>>>> Also, apart from this one error, I notice another error: >>>>> ERROR: Non-unique top level ID for chr5:hit:1454:4_0 >>>>> While this is technically legal in GFF3, it usually >>>>> indicates a poorly fomatted GFF3 file (perhaps you >>>>> tried to merge two GFF3 files without accounting for >>>>> unique IDs). MAKER will not handle these correctly. >>>>> >>>>> On inspecting the input GFF file (protein2genome), I see that this ID is >>>>> never repeated. So I have no idea whats going on here either. Any >>>>> suggestions? >>>>> >>>>> Below is my `maker.err` file from the run. (Dropbox link) >>>>> >>>>> Thank you very much. >>>>> Best, >>>>> >>>>> Vivek >>>>> >>>>> -- >>>>> Vivek Krishnakumar >>>>> vkrishnakumar at jcvi.org >>>>> >>>>> >>>>> >>>>> I've linked 1 file to this email: >>>>> >>>>> >>>>> maker.err (97.7 MB)Dropbox >>>>> http://db.tt/2tYyKCD7 >>>>> >>>>> >>>>> Mozilla Thunderbird makes it easy to >>>>> share large files over email. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> _______________________________________________ maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >>> >> >> >> >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From ranjani at uga.edu Thu Jan 24 22:17:13 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Fri, 25 Jan 2013 05:17:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: , Message-ID: I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam > Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" > Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 11:43:17 2013 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2013 13:43:17 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Also since single exon ESTs are almost always coming from background transcription and not real genes, MAKER may also require some sort of protein alignment or ab initio predictor support before promoting them to gene models. --Carson From: Sivaranjani Namasivayam Date: Friday, 25 January, 2013 12:17 AM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] Transcriptome data to gene models I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Tue Jan 29 09:50:24 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 29 Jan 2013 09:50:24 -0700 Subject: [maker-devel] Fwd: Help in installation of MAKER2 References: Message-ID: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 09:57:25 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 11:57:25 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: If it is a 64 bit Intel Mac make sure you install the 64 bit version of fink and not the 32 bit version. Then use fink to install both of these --> glib2-dev glib2-shlibs Installing them any other way on a Mac makes it so much harder to get the configuration right. Do 'fink remove' if you've already installed them with fink, then update fink and make sure it is the right fink for your processor before reinstalling. --Carson From: Barry Moore Date: Tuesday, 29 January, 2013 11:50 AM To: Maker Mailing List Cc: Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Jan 29 09:58:57 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 29 Jan 2013 16:58:57 +0000 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> References: , <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 Date: January 29, 2013 4:45:49 AM MST To: > Hi Barry, I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: checking for socklen_t... yes checking for pkg-config... no ERROR: Could not find pkg-config ... is glib-2 installed ??? macpro:exonerate-2.2.0 admin$ pkg-get -bash: pkg-get: command not found I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 10:04:54 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 12:04:54 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: Message-ID: I had problems moving from OS X 10.5 to 10.6 and from 10.6 to 10.7. All of which were solved by reinstalling fink (for the right processor ? 32bit vs 64bit) and all tools and libraries I had from fink. Thanks, Carson From: Daniel Ence Date: Tuesday, 29 January, 2013 11:58 AM To: Maker Mailing List , Carson Holt Cc: "alexmendozasoler at gmail.com" Subject: RE: [maker-devel] Fwd: Help in installation of MAKER2 Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:09:23 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:09:23 +0100 Subject: [maker-devel] Compilation Problems Message-ID: <50ED8823.8050001@uni-wuerzburg.de> Hi, I am trying to compile maker (2.27-beta) with MPI support on Ubuntu 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and a self compiled version (MPICH2 3.0.1) at hand. The latter one was compiled with the -enable-shared flag. I got the following error during the maker install command with both versions: Configuring MAKER with MPI support /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc MPI.c /software/mpich/bin/mpicc -c -I"/storage/software/intel64/maker-2.27-beta/src" -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c MPI.xs: In Funktion ?_MPI_Send?: MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? von inkompatiblem Zeigertyp [standardm??ig aktiviert] /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? erwartet, aber Argument hat Typ ?int *? Running Mkbootstrap for Parallel::Application::MPI () chmod 644 MPI.bs rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib -fstack-protector MPI.o -o blib/arch/auto/Parallel/Application/MPI/MPI.so \ \ /usr/bin/ld: /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when making a shared object; recompile with -fPIC /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read symbols: Bad value collect2: ld gab 1 als Ende-Status zur?ck make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make > out.make 2>&1 The build directory was: /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Application/MPI To debug the problem, cd to the build directory, and inspect the output files. at /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Application/MPI.pm line 223 Does anybody have an idea, what is happening here? Best regards Felix -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:18:06 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:18:06 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED8823.8050001@uni-wuerzburg.de> Message-ID: It is a problem with compilation of the shared libraries in MPICH2. You can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and CXXFLAGS environmental variables. Alternatively I would recommend not using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it is the new MPICH3. It is their first attempt to provide full support of the new MPI-3 standard, so compared to other MPICH2 releases which all use the MPI-2 standard it will be very buggy. So avoid it unless your inner geek loves the pain that comes from working with bleeding edge advances. I would recommend using the last release of MPICH2 which was version 1.5. Thanks, Carson On 13-01-09 10:09 AM, "Felix Bemm" wrote: >Hi, > >I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >a self compiled version (MPICH2 3.0.1) at hand. The latter one was >compiled with the -enable-shared flag. I got the following error during >the maker install command with both versions: > >Configuring MAKER with MPI support >/usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >"/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >MPI.c >/software/mpich/bin/mpicc -c >-I"/storage/software/intel64/maker-2.27-beta/src" >-I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >MPI.xs: In Funktion ?_MPI_Send?: >MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >von inkompatiblem Zeigertyp [standardm??ig aktiviert] >/usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >erwartet, aber Argument hat Typ ?int *? >Running Mkbootstrap for Parallel::Application::MPI () >chmod 644 MPI.bs >rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >/software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >-fstack-protector MPI.o -o >blib/arch/auto/Parallel/Application/MPI/MPI.so \ > \ > >/usr/bin/ld: >/storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >making a shared object; recompile with -fPIC >/storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >symbols: Bad value >collect2: ld gab 1 als Ende-Status zur?ck >make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 > >A problem was encountered while attempting to compile and install your >Inline >C code. The command that failed was: > make > out.make 2>&1 > >The build directory was: >/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >ion/MPI > >To debug the problem, cd to the build directory, and inspect the output >files. > > at >/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >tion/MPI.pm >line 223 > >Does anybody have an idea, what is happening here? > >Best regards >Felix > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From felix.bemm at uni-wuerzburg.de Wed Jan 9 08:53:21 2013 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Wed, 09 Jan 2013 16:53:21 +0100 Subject: [maker-devel] Compilation Problems In-Reply-To: References: Message-ID: <50ED9271.8090300@uni-wuerzburg.de> Thanks Carson, version change (to mpich2 1.5) fixed the problem. I did not realize that I was downloading some mpich3 after all. Thanks again for the fast help! Best regards Felix On 09.01.2013 16:18, Carson Holt wrote: > It is a problem with compilation of the shared libraries in MPICH2. You > can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and > CXXFLAGS environmental variables. Alternatively I would recommend not > using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it > is the new MPICH3. It is their first attempt to provide full support of > the new MPI-3 standard, so compared to other MPICH2 releases which all use > the MPI-2 standard it will be very buggy. So avoid it unless your inner > geek loves the pain that comes from working with bleeding edge advances. > I would recommend using the last release of MPICH2 which was version 1.5. > > Thanks, > Carson > > > On 13-01-09 10:09 AM, "Felix Bemm" wrote: > >> Hi, >> >> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >> compiled with the -enable-shared flag. I got the following error during >> the maker install command with both versions: >> >> Configuring MAKER with MPI support >> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv MPI.xsc >> MPI.c >> /software/mpich/bin/mpicc -c >> -I"/storage/software/intel64/maker-2.27-beta/src" >> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >> MPI.xs: In Funktion ?_MPI_Send?: >> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >> erwartet, aber Argument hat Typ ?int *? >> Running Mkbootstrap for Parallel::Application::MPI () >> chmod 644 MPI.bs >> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >> -fstack-protector MPI.o -o >> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >> \ >> >> /usr/bin/ld: >> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >> making a shared object; recompile with -fPIC >> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >> symbols: Bad value >> collect2: ld gab 1 als Ende-Status zur?ck >> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >> >> A problem was encountered while attempting to compile and install your >> Inline >> C code. The command that failed was: >> make > out.make 2>&1 >> >> The build directory was: >> /storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat >> ion/MPI >> >> To debug the problem, cd to the build directory, and inspect the output >> files. >> >> at >> /storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica >> tion/MPI.pm >> line 223 >> >> Does anybody have an idea, what is happening here? >> >> Best regards >> Felix >> >> -- >> Felix Bemm >> Department of Bioinformatics >> University of W?rzburg, Germany >> Tel: +49 931 - 31 83696 >> Fax: +49 931 - 31 84552 >> felix.bemm at uni-wuerzburg.de >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From carsonhh at gmail.com Wed Jan 9 08:49:51 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 09 Jan 2013 10:49:51 -0500 Subject: [maker-devel] Compilation Problems In-Reply-To: <50ED9271.8090300@uni-wuerzburg.de> Message-ID: I'm Glad it worked. Thanks, Carson On 13-01-09 10:53 AM, "Felix Bemm" wrote: >Thanks Carson, > >version change (to mpich2 1.5) fixed the problem. I did not realize that >I was downloading some mpich3 after all. Thanks again for the fast help! > >Best regards >Felix > >On 09.01.2013 16:18, Carson Holt wrote: >> It is a problem with compilation of the shared libraries in MPICH2. You >> can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS >>and >> CXXFLAGS environmental variables. Alternatively I would recommend not >> using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it >> is the new MPICH3. It is their first attempt to provide full support of >> the new MPI-3 standard, so compared to other MPICH2 releases which all >>use >> the MPI-2 standard it will be very buggy. So avoid it unless your inner >> geek loves the pain that comes from working with bleeding edge advances. >> I would recommend using the last release of MPICH2 which was version >>1.5. >> >> Thanks, >> Carson >> >> >> On 13-01-09 10:09 AM, "Felix Bemm" wrote: >> >>> Hi, >>> >>> I am trying to compile maker (2.27-beta) with MPI support on Ubuntu >>> 12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and >>> a self compiled version (MPICH2 3.0.1) at hand. The latter one was >>> compiled with the -enable-shared flag. I got the following error during >>> the maker install command with both versions: >>> >>> Configuring MAKER with MPI support >>> /usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp -typemap >>> "/usr/share/perl/5.14/ExtUtils/typemap" MPI.xs > MPI.xsc && mv >>>MPI.xsc >>> MPI.c >>> /software/mpich/bin/mpicc -c >>> -I"/storage/software/intel64/maker-2.27-beta/src" >>> -I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >>> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\" >>> -DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE" MPI.c >>> MPI.xs: In Funktion ?_MPI_Send?: >>> MPI.xs:42:5: Warnung: ?bergabe des Arguments 3 von ?Perl_sv_2pv_flags? >>> von inkompatiblem Zeigertyp [standardm??ig aktiviert] >>> /usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: ?STRLEN * const? >>> erwartet, aber Argument hat Typ ?int *? >>> Running Mkbootstrap for Parallel::Application::MPI () >>> chmod 644 MPI.bs >>> rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so >>> /software/mpich/bin/mpicc -shared -O2 -g -L/usr/local/lib >>> -fstack-protector MPI.o -o >>> blib/arch/auto/Parallel/Application/MPI/MPI.so \ >>> \ >>> >>> /usr/bin/ld: >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o): >>> relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when >>> making a shared object; recompile with -fPIC >>> /storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read >>> symbols: Bad value >>> collect2: ld gab 1 als Ende-Status zur?ck >>> make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1 >>> >>> A problem was encountered while attempting to compile and install your >>> Inline >>> C code. The command that failed was: >>> make > out.make 2>&1 >>> >>> The build directory was: >>> >>>/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applic >>>at >>> ion/MPI >>> >>> To debug the problem, cd to the build directory, and inspect the output >>> files. >>> >>> at >>> >>>/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Appli >>>ca >>> tion/MPI.pm >>> line 223 >>> >>> Does anybody have an idea, what is happening here? >>> >>> Best regards >>> Felix >>> >>> -- >>> Felix Bemm >>> Department of Bioinformatics >>> University of W?rzburg, Germany >>> Tel: +49 931 - 31 83696 >>> Fax: +49 931 - 31 84552 >>> felix.bemm at uni-wuerzburg.de >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >-- >Felix Bemm >Department of Bioinformatics >University of W?rzburg, Germany >Tel: +49 931 - 31 83696 >Fax: +49 931 - 31 84552 >felix.bemm at uni-wuerzburg.de > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From ranjani at uga.edu Wed Jan 16 09:16:27 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 16 Jan 2013 16:16:27 +0000 Subject: [maker-devel] Transcriptome data to gene models Message-ID: Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Wed Jan 16 10:19:13 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 16 Jan 2013 17:19:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Wed Jan 16 10:24:08 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 16 Jan 2013 17:24:08 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From barry.moore at genetics.utah.edu Wed Jan 16 11:07:57 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 16 Jan 2013 10:07:57 -0800 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF@CHIMBX5.ad.uillinois.edu> Message-ID: Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Jan 16 11:16:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 16 Jan 2013 13:16:15 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Wed Jan 16 11:26:12 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Wed, 16 Jan 2013 18:26:12 +0000 Subject: [maker-devel] Txome annotation Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA0415B8DE@EXCHANGE-05.internal.solazyme.com> Does anyone have a good suggestion for annotating transcriptomes? In particular calling ORFs (like the best ORF, not just a simple longest ORF) and doing functional annotation? I am currently using cd-hit to try and get a representative transcript set, but I want somthing similar in the ORF space that attempts to call the best, and alternative, ORFs. I am using AutoFact to do functional annotation, and it works, but I don't think it is under continued development. Thanks, Shane ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of maker-devel-request at yandell-lab.org [maker-devel-request at yandell-lab.org] Sent: Wednesday, January 16, 2013 10:16 AM To: maker-devel at yandell-lab.org Subject: maker-devel Digest, Vol 56, Issue 2 Send maker-devel mailing list submissions to maker-devel at yandell-lab.org To subscribe or unsubscribe via the World Wide Web, visit http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org or, via email, send a message with subject or body 'help' to maker-devel-request at yandell-lab.org You can reach the person managing the list at maker-devel-owner at yandell-lab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of maker-devel digest..." Today's Topics: 1. Transcriptome data to gene models (Sivaranjani Namasivayam) 2. Re: Transcriptome data to gene models (Daniel Ence) 3. Re: Transcriptome data to gene models (Fields, Christopher J) 4. Re: Transcriptome data to gene models (Barry Moore) 5. Re: Transcriptome data to gene models (Carson Holt) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Jan 2013 16:16:27 +0000 From: Sivaranjani Namasivayam To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 16 Jan 2013 17:19:13 +0000 From: Daniel Ence To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Ranjani, Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Wednesday, January 16, 2013 9:16 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 16 Jan 2013 17:24:08 +0000 From: "Fields, Christopher J" To: Daniel Ence Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BF2CEF at CHIMBX5.ad.uillinois.edu> Content-Type: text/plain; charset="iso-8859-1" I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? chris On Jan 16, 2013, at 11:19 AM, Daniel Ence wrote: > Hi Ranjani, > > Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] > Sent: Wednesday, January 16, 2013 9:16 AM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Transcriptome data to gene models > > Hi, > > I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors > But I find gene models are not generated for all transcripts only about half of them. > > Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? > > Thanks, > Ranjani > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org ------------------------------ Message: 4 Date: Wed, 16 Jan 2013 10:07:57 -0800 From: Barry Moore To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome as evidence (no gene prediction, possibly no BLAST). Note he mentioned setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome annotation is very different from genome annotation. I think probably some of your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half of them. >> >> Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 16 Jan 2013 13:16:15 -0500 From: Carson Holt To: Barry Moore , Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Message-ID: Content-Type: text/plain; charset="us-ascii" Yes. Change single_exon=0 to single_exon=1. --Carson From: Barry Moore Date: Wednesday, 16 January, 2013 1:07 PM To: Maker Mailing List Subject: Re: [maker-devel] Transcriptome data to gene models Ranhani, Are the transcripts for which no annotation is created all single exon? With any predictor (est2genome included) you need some physical alignment evidence for Maker to promote it to an annotation. In the case of using est2genome as the only predictor it's a bit odd to think of it that way since Maker is using the same data to predict a model and as evidence to support it. However by default Maker requires EITHER a spliced transcript OR protein evidence to support the model before it becomes a Maker annotation. Thus with only est2genome and no protein evidence you will never annotate a single exon gene (by default). If this is indeed the case for you, you may want to consider the use of the following options: single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no single_length=250 #min length required for single exon ESTs if 'single_exon is enabled' Barry On Jan 16, 2013, at 9:24 AM, Fields, Christopher J wrote: > I think he is annotating a genome, but only using an available transcriptome > as evidence (no gene prediction, possibly no BLAST). Note he mentioned > setting est2genome. > > Is it possible that this is due to est2genome and not MAKER (e.g. est2genome > is mapping only half of your transcriptome data)? > > chris > > On Jan 16, 2013, at 11:19 AM, Daniel Ence > wrote: > >> Hi Ranjani, >> >> Maker was designed to annotate genomes, not transcriptomes. Transcriptome >> annotation is very different from genome annotation. I think probably some of >> your transcripts are just too short maker to work with. >> >> Thanks, >> Daniel >> >> Daniel Ence >> Graduate Student >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> From: maker-devel-bounces at yandell-lab.org >> [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam >> [ranjani at uga.edu] >> Sent: Wednesday, January 16, 2013 9:16 AM >> To: maker-devel at yandell-lab.org >> Subject: [maker-devel] Transcriptome data to gene models >> >> Hi, >> >> I want to generate gene models for all my transcripts (based on just the >> transcript evidence). To do this I set 'est2genome to gene models' attribute >> to 1. I have disabled gene predictions from any another sources, that is, I >> do not provide protein data and turned off all gene predictors >> But I find gene models are not generated for all transcripts only about half >> of them. >> >> Can you tell me how maker decides which transcripts to predict models for, >> that is, how is it making this selective decision? >> >> Thanks, >> Ranjani >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org End of maker-devel Digest, Vol 56, Issue 2 ****************************************** From kapeelc at gmail.com Fri Jan 18 12:00:42 2013 From: kapeelc at gmail.com (Kapeel Chougule) Date: Fri, 18 Jan 2013 12:00:42 -0700 Subject: [maker-devel] BLAST options error Message-ID: Hi, I had this error for one of the chromosomes: BLAST options error: /opt/kapeel/maker_runs/leersia/chr11/Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/comp84263_c0_seq4.for_blastn.fasta does not match input format type, default input type is FASTA ERROR: Failed while collecting blastn reports ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:Chr11 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:Chr11 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Chr11.maker.output/Chr11_datastore/1E/AA/Chr11//theVoid.Chr11/Chr11.286769.311208.0.comp84263_c0_seq4%2Efor_blastn%2Efasta.blastn did not finish on the last run and must be erased Maker is now finished!!! I checked the comp84263_c0_seq4.for_blastn.fasta file for any spaces before > symbol in the header section, it seems to be ok with that. Any suggestions? Thank you, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu From mikael.durling at slu.se Tue Jan 22 02:56:45 2013 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 22 Jan 2013 09:56:45 +0000 Subject: [maker-devel] maker_map_ids anomaly Message-ID: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Hi, I'm trying to load maker annotations into JBrowse, however, the flat file loader can't parse the maker gff stating "parse error: orphans". Looking into one of the broken maker transcripts, it looks like below. Note that the two different mRNAs get the same ID, but a different name. The lines from maker_map_ids are pasted below too. This was a re-annotation run of a previous maker run, which was id_mapped before being used as maker_gff in the current run with model_pass=1 in order to preserve gene names. (btw, loading the unmapped initial maker run into jbrowse works fine.) scf_89829 maker gene 38002 41976 . + . ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; scf_89829 maker mRNA 38002 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=CROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=436|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; scf_89829 maker mRNA 38611 41976 . + . ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=maker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33|3|1149|602;_eAED=0.06;Note=Protein of unknown function; scf_89829 maker exon 38002 38349 . + . ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; scf_89829 maker exon 38872 39702 . + . ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 39762 41976 . + . ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; scf_89829 maker exon 38611 38647 . + . ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38002 38349 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; scf_89829 maker five_prime_UTR 38611 38647 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker five_prime_UTR 38872 38959 . + . ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; scf_89829 maker CDS 38960 39702 . + 0 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker CDS 39762 40827 . + 1 ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; scf_89829 maker three_prime_UTR 40828 41976 . + . ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; Related id map lines: CROS1_G00002820 CROS1_G00002820 maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 CROS1_T00002820_1 CROS1_T00002820_2 and the command line for maker_map_ids: maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ --iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > CrosV1.maker.output/CrosV1.id_map thanks for any hints, Mikael From carsonhh at gmail.com Wed Jan 23 07:42:08 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:42:08 -0700 Subject: [maker-devel] maker_map_ids anomaly In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C607F68EED@exchange2-2> Message-ID: So does the problem occur immediately following the maker_map_ids step or does it occur after running maker before the maker_map_ids step. I ask so I can identify if it is the maker_map_ids script I neeed to debug or maker. Could you send me the GFF3 file imediatley preceding the step where the error originate. Thanks, Carson On 13-01-22 2:56 AM, "Mikael Brandstr?m Durling" wrote: >Hi, > >I'm trying to load maker annotations into JBrowse, however, the flat file >loader can't parse the maker gff stating "parse error: orphans". Looking >into one of the broken maker transcripts, it looks like below. Note that >the two different mRNAs get the same ID, but a different name. The lines >from maker_map_ids are pasted below too. This was a re-annotation run of >a previous maker run, which was id_mapped before being used as maker_gff >in the current run with model_pass=1 in order to preserve gene names. >(btw, loading the unmapped initial maker run into jbrowse works fine.) > >scf_89829 maker gene 38002 41976 . + . >ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function; >scf_89829 maker mRNA 38002 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=C >ROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=4 >36|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function; >scf_89829 maker mRNA 38611 41976 . + . >ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=m >aker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33| >3|1149|602;_eAED=0.06;Note=Protein of unknown function; >scf_89829 maker exon 38002 38349 . + . >ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1; >scf_89829 maker exon 38872 39702 . + . >ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 39762 41976 . + . >ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2; >scf_89829 maker exon 38611 38647 . + . >ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38002 38349 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1; >scf_89829 maker five_prime_UTR 38611 38647 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker five_prime_UTR 38872 38959 . + . > ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 38960 39702 . + 0 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker CDS 39762 40827 . + 1 >ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2; >scf_89829 maker three_prime_UTR 40828 41976 . + . > ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2; > > >Related id map lines: > >CROS1_G00002820 CROS1_G00002820 >maker-scf_89829-augustus-gene-0.68-mRNA-1 CROS1_T00002820_1 >CROS1_T00002820_1 CROS1_T00002820_2 > > >and the command line for maker_map_ids: > >maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ >--iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > >CrosV1.maker.output/CrosV1.id_map > >thanks for any hints, >Mikael >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Wed Jan 23 07:59:39 2013 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 23 Jan 2013 07:59:39 -0700 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Wed Jan 23 08:31:46 2013 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 23 Jan 2013 10:31:46 -0500 Subject: [maker-devel] Question about AED scores Message-ID: Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the *_AED* attribute, which leads to my other question: what does the value of the *_eAED* attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Wed Jan 23 12:42:42 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Wed, 23 Jan 2013 14:42:42 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Message-ID: <51003D32.4080908@jcvi.org> Hello, I'm trying to use the MAKER pipeline to calculate AED scores for the gene models coming out of our annotation pipeline (EVidence Modeler). We then want to compare these computed AED scores with those computed for the gene models coming out of the MAKER2 pipeline. For this purpose, I configured the maker_opts.ctl file like so: 1) Specify gff file coming from our annotation pipeline using `model_gff` param 2) Specify gff file containing est2genome results (computed using MAKER2) using the `est_gff` param 3) Specify gff file containing protein2genome results (computed using MAKER2) using the `protein_gff` param 4) Specify the genome fasta sequence file using the `genome` param I recently configured MAKER 2.27b to work using MPI and I tried launching one contig (chromosome) on a compute node spawning 12 processes like so: mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err Side note: Without MPI, it works fine but takes very very long to complete running on one chromosome (since it is going through the chunks serially). On inspecting the `maker.err` file, I see server error messages that say `DBD::SQLite::db do failed: database is locked`. On referring to a previous email thread on the `maker-devel` mailing list, I see that Carson had replied to the person with a similar issue asking them to check if the working directory and TMP directory are being mounted on an NFS filesystem because this is a potential problem with SQLite databases. Based on that suggestion, I switched the TMP directory to use a local filesytem but the working directory is still NFS mounted. Despite that, I still get this error. The previous email thread had no resolution for this issue. My question is, should the working directory be local as well? I see that despite setting the `TMP` variable, the SQLite DB is getting created in the working directory. What might be the issue? Also, apart from this one error, I notice another error: ERROR: Non-unique top level ID for chr5:hit:1454:4_0 While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. On inspecting the input GFF file (protein2genome), I see that this ID is never repeated. So I have no idea whats going on here either. Any suggestions? Below is my `maker.err` file from the run. (Dropbox link) Thank you very much. Best, Vivek -- Vivek Krishnakumar vkrishnakumar at jcvi.org I've linked 1 file to this email: maker.err (97.7 MB)Dropbox http://db.tt/2tYyKCD7 Mozilla Thunderbird makes it easy to share large files over email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: attachment-24.png Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dropbox.png Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 12:02:12 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 14:02:12 -0500 Subject: [maker-devel] Question about AED scores In-Reply-To: Message-ID: AED from MAKER in the based on nucleotide-level congruency of the transcript compared to the collapsed evidence. eAED is also at the nucleotide level but is adjusted for inferred support of exons, such as can happen with mRNAseq (I.e. I can confirm the splice sites at each end but as the exon gets longer the middle is less likely to be covered). So if I can infer the middle based on ORF and the splice site are confirmed then I consider the middle of the exon to be confirmed for calculating eAED. eAED also adjusts for reading frame from protein evidence alignments, i.e. protein overlap in a different reading frame than the final gene model will not contribute to eAED. So because of this, eAED takes much longer to calculate but is sometimes more useful. Much of the time AED and eAED are identical. Thanks, Carson From: Daniel Standage Date: Wednesday, 23 January, 2013 10:31 AM To: Maker Mailing List Subject: [maker-devel] Question about AED scores Good morning! I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct? I'm assuming this score is stored in the _AED attribute, which leads to my other question: what does the value of the _eAED attribute represent? Is this the same score calculated at the exon level? Many thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From vkrishnakumar at jcvi.org Thu Jan 24 12:49:36 2013 From: vkrishnakumar at jcvi.org (Krishnakumar, Vivek) Date: Thu, 24 Jan 2013 14:49:36 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51003D32.4080908@jcvi.org> References: <51003D32.4080908@jcvi.org> Message-ID: <51019050.1030003@jcvi.org> Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the > gene models coming out of our annotation pipeline (EVidence Modeler). > We then want to compare these computed AED scores with those computed > for the gene models coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using > `model_gff` param > 2) Specify gff file containing est2genome results (computed using > MAKER2) using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using > MAKER2) using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried > launching one contig (chromosome) on a compute node spawning 12 > processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to > complete running on one chromosome (since it is going through the > chunks serially). > > On inspecting the `maker.err` file, I see server error messages that > say `DBD::SQLite::db do failed: database is locked`. On referring to a > previous email thread on the `maker-devel` mailing list, I see that > Carson had replied to the person with a similar issue asking them to > check if the working directory and TMP directory are being mounted on > an NFS filesystem because this is a potential problem with SQLite > databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite > that, I still get this error. The previous email thread had no > resolution for this issue. My question is, should the working > directory be local as well? I see that despite setting the `TMP` > variable, the SQLite DB is getting created in the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID > is never repeated. So I have no idea whats going on here either. Any > suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > I've linked 1 file to this email: > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > Mozilla Thunderbird makes it easy to > share large files over email. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1205 bytes Desc: not available URL: From carsonhh at gmail.com Thu Jan 24 13:02:58 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:02:58 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <51019050.1030003@jcvi.org> Message-ID: If you still see issue, let me know. I have a hard time seeing how just moving to MPICH2 would have solved the issue. It may also have been an initial problem with the first GFF# db being created and running on a new job recreated it correctly. Either way, let me know if it comes up on your bigger run. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 2:49 PM To: , Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Hi Everybody, Sorry for jumping the gun and writing to the mailing list before completely troubleshooting this issue. I was able to figure out the problem and get MAKER 2.27b working fine in MPI mode. The issue was with the incorrect version of mpicc (it was openMPI based and not mpich2). I was able to successfully run through the steps described below on one chromosome in under a few hours (~2). Now I'm scaling it to the whole genome (8 chromosomes and ~2200 unanchored scaffolds). Thank you. Vivek On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: > Hello, > > I'm trying to use the MAKER pipeline to calculate AED scores for the gene > models coming out of our annotation pipeline (EVidence Modeler). We then want > to compare these computed AED scores with those computed for the gene models > coming out of the MAKER2 pipeline. > > For this purpose, I configured the maker_opts.ctl file like so: > 1) Specify gff file coming from our annotation pipeline using `model_gff` > param > 2) Specify gff file containing est2genome results (computed using MAKER2) > using the `est_gff` param > 3) Specify gff file containing protein2genome results (computed using MAKER2) > using the `protein_gff` param > 4) Specify the genome fasta sequence file using the `genome` param > > I recently configured MAKER 2.27b to work using MPI and I tried launching one > contig (chromosome) on a compute node spawning 12 processes like so: > mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl > maker_exe.ctl 2>&1 | tee maker.err > > Side note: Without MPI, it works fine but takes very very long to complete > running on one chromosome (since it is going through the chunks serially). > > On inspecting the `maker.err` file, I see server error messages that say > `DBD::SQLite::db do failed: database is locked`. On referring to a previous > email thread on the `maker-devel` mailing list, I see that Carson had replied > to the person with a similar issue asking them to check if the working > directory and TMP directory are being mounted on an NFS filesystem because > this is a potential problem with SQLite databases. > > Based on that suggestion, I switched the TMP directory to use a local > filesytem but the working directory is still NFS mounted. Despite that, I > still get this error. The previous email thread had no resolution for this > issue. My question is, should the working directory be local as well? I see > that despite setting the `TMP` variable, the SQLite DB is getting created in > the working directory. > > What might be the issue? > > Also, apart from this one error, I notice another error: > ERROR: Non-unique top level ID for chr5:hit:1454:4_0 > While this is technically legal in GFF3, it usually > indicates a poorly fomatted GFF3 file (perhaps you > tried to merge two GFF3 files without accounting for > unique IDs). MAKER will not handle these correctly. > > On inspecting the input GFF file (protein2genome), I see that this ID is > never repeated. So I have no idea whats going on here either. Any suggestions? > > Below is my `maker.err` file from the run. (Dropbox link) > > Thank you very much. > Best, > > Vivek > > -- > Vivek Krishnakumar > vkrishnakumar at jcvi.org > > > > I've linked 1 file to this email: > > > maker.err (97.7 MB)Dropbox > http://db.tt/2tYyKCD7 > > > Mozilla Thunderbird makes it easy to share > large files over email. > > > _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From sbrubaker at solazyme.com Thu Jan 24 13:17:57 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:17:57 +0000 Subject: [maker-devel] Maker-P Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Hi, I heard about Maker-P at PAG. We are working on an algae, which is closer to plants than just about anything else - I am wondering, would Maker-P be useful for us to use instead of regular Maker? From carsonhh at gmail.com Thu Jan 24 13:31:28 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 15:31:28 -0500 Subject: [maker-devel] FW: Maker-P In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From michael.s.campbell1 at gmail.com Thu Jan 24 13:47:20 2013 From: michael.s.campbell1 at gmail.com (Michael Campbell) Date: Thu, 24 Jan 2013 13:47:20 -0700 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt wrote: > I'm forwarding this to the most relevant people. > > --Carson > > > On 13-01-24 3:17 PM, "Shane Brubaker" wrote: > > >Hi, I heard about Maker-P at PAG. We are working on an algae, which is > >closer to plants than just about anything else - I am wondering, would > >Maker-P be useful for us to use instead of regular Maker? > > > >_______________________________________________ > >maker-devel mailing list > >maker-devel at box290.bluehost.com > >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrubaker at solazyme.com Thu Jan 24 13:48:19 2013 From: sbrubaker at solazyme.com (Shane Brubaker) Date: Thu, 24 Jan 2013 20:48:19 +0000 Subject: [maker-devel] FW: Maker-P In-Reply-To: References: <61D01ACB70C1E141A150BA9F586D5BFA04B234AD@EXCHANGE-MB01.internal.solazyme.com> Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA04B23517@EXCHANGE-MB01.internal.solazyme.com> Ok that makes sense - Thanks! Sincerely, Shane Brubaker Director of BioInformatics Solazyme, Inc. 225 Gateway Blvd. S. San Francisco, CA 94080 From: Michael Campbell [mailto:michael.s.campbell1 at gmail.com] Sent: Thursday, January 24, 2013 12:47 PM To: Carson Holt Cc: Shane Brubaker; MeiYee Law; Mark Yandell; Maker Mailing List Subject: Re: FW: [maker-devel] Maker-P Hi all, I'l' take a shot at answering this one. MAKER-P is largely a project name and represents our efforts to benchmark and improve MAKER's performance on plants. The version 2.27 release of MAKER has bug fixes and performance enhancements incorporated as a result of things we learned while bench marking MAKER on arabidopsis and maize; and the de novo annotation of sacred lotus and the algae Nannochloropsis. These changes did not impair MAKER's performance on animal genomes, so at this point we have opted not to maintain two versions of MAKER. Other people on the project are welcome to weigh in if they would like. Mike On Thu, Jan 24, 2013 at 1:31 PM, Carson Holt > wrote: I'm forwarding this to the most relevant people. --Carson On 13-01-24 3:17 PM, "Shane Brubaker" > wrote: >Hi, I heard about Maker-P at PAG. We are working on an algae, which is >closer to plants than just about anything else - I am wondering, would >Maker-P be useful for us to use instead of regular Maker? > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Michael Campbell MS, RD. Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 24 14:39:15 2013 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 24 Jan 2013 16:39:15 -0500 Subject: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI In-Reply-To: <5101A7D6.4070101@jcvi.org> Message-ID: Done. Thanks, Carson From: "Krishnakumar, Vivek" Date: Thursday, 24 January, 2013 4:29 PM To: Carson Holt Cc: "mcampbell at genetics.utah.edu" Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI Ok. Seems to be working fine. I pointed the TMP parameter to our scratch area. Thanks for your suggestion. Should I forward this conversation thread to the maker-devel list ? Vivek On 01/24/2013 04:08 PM, Carson Holt wrote: > > SQLlite will choke almost immediately if it's not set up with the correct > flags, so you will know right away. > > > > > --Carson > > > > > From: "Krishnakumar, Vivek" > Date: Thursday, 24 January, 2013 3:35 PM > To: Carson Holt > Cc: "mcampbell at genetics.utah.edu" > Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked > (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI > > > > > > > Okay. I will try doing that. But how can I find out that my NFS mounted area > has -nolock set? The filesystem areas that we work on are managed by our IT > department. > > Thanks. > Vivek > > > On 01/24/2013 03:27 PM, Carson Holt wrote: > > >> >> If you don't have locally mounted space big enough, then just use an NFS >> mounted /TMP. You will take a slight performance hit, but it may still work >> if it is mounted with -nolock set so SQLite stops complaining. >> >> >> >> >> --Carson >> >> >> >> >> From: "Krishnakumar, Vivek" >> Date: Thursday, 24 January, 2013 3:24 PM >> To: Carson Holt >> Cc: "mcampbell at genetics.utah.edu" >> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >> >> >> >> >> >> >> I no longer see that warning. >> >> The only thing I see is that MAKER now complains that the DB is corrupt, and >> that is because I only have 5GB of /tmp space on the server I currently have >> access to and that is not enough for the whole genome FASTA + est2genome + >> protein2genome + model_gff (EVM). >> >> Thanks, >> Vivek >> >> >> >> On 01/24/2013 03:20 PM, Carson Holt wrote: >> >> >>> >>> You should be able to run on an NFS drive. After creating the initial >>> SQLite database, maker now gives each node it's own copy that is stored in >>> the TMP directory (should be local to each node). Could you send me the >>> GFF3 file that gives the warning, so I can look at it. >>> >>> >>> >>> >>> Thanks, >>> >>> Carson >>> >>> >>> >>> >>> >>> >>> >>> From: "Krishnakumar, Vivek" >>> Date: Thursday, 24 January, 2013 3:17 PM >>> To: Carson Holt >>> Cc: "mcampbell at genetics.utah.edu" >>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>> >>> >>> >>> >>> >>> >>> Hi Carson, >>> >>> I did make sure that every time I reran the pipeline, I deleted the >>> maker.output directory and the temporary files in /tmp. That way I know that >>> the DBs get created fresh. >>> >>> When it was openMPI based, I noticed that irrespective of whether I enabled >>> or disabled the `-TMP` parameter, I would get the database locked error. At >>> this point, mpicc was openMPI based and mpiexec (hydra) was MPICH2 based. >>> >>> On installing MPICH2 as a non-root user and rebuilding `maker`, this issue >>> vanished. Just an observation. >>> >>> The issue I have now with scaling up is that I do not currently have access >>> to a server that has a large amount of non-NFS mounted storage space (we do >>> have such a server but it has been reserved for a different project by a >>> group in our institute). Thus, the creation of the SQLite db is halted mid >>> way and now MAKER complains that the database is corrupt. I can either run >>> the chromosomes individually (serially) and then the scaffolds as one group >>> or wait to get a time slot of that server. >>> >>> Will let you know if I have any more issues. >>> >>> Thank you. >>> Vivek >>> >>> >>> >>> On 01/24/2013 03:02 PM, Carson Holt wrote: >>> >>> >>>> >>>> If you still see issue, let me know. I have a hard time seeing how just >>>> moving to MPICH2 would have solved the issue. It may also have been an >>>> initial problem with the first GFF# db being created and running on a new >>>> job recreated it correctly. Either way, let me know if it comes up on your >>>> bigger run. >>>> >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Carson >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> From: "Krishnakumar, Vivek" >>>> Date: Thursday, 24 January, 2013 2:49 PM >>>> To: , >>>> Subject: Re: [maker-devel] DBD::SQLite::db do failed: database is locked >>>> (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI >>>> >>>> >>>> >>>> >>>> >>>> >>>> Hi Everybody, >>>> >>>> Sorry for jumping the gun and writing to the mailing list before >>>> completely troubleshooting this issue. I was able to figure out the problem >>>> and get MAKER 2.27b working fine in MPI mode. >>>> >>>> The issue was with the incorrect version of mpicc (it was openMPI based >>>> and not mpich2). I was able to successfully run through the steps described >>>> below on one chromosome in under a few hours (~2). Now I'm scaling it to >>>> the whole genome (8 chromosomes and ~2200 unanchored scaffolds). >>>> >>>> Thank you. >>>> Vivek >>>> >>>> >>>> On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote: >>>> >>>> >>>>> Hello, >>>>> >>>>> I'm trying to use the MAKER pipeline to calculate AED scores for the gene >>>>> models coming out of our annotation pipeline (EVidence Modeler). We then >>>>> want to compare these computed AED scores with those computed for the gene >>>>> models coming out of the MAKER2 pipeline. >>>>> >>>>> For this purpose, I configured the maker_opts.ctl file like so: >>>>> 1) Specify gff file coming from our annotation pipeline using `model_gff` >>>>> param >>>>> 2) Specify gff file containing est2genome results (computed using MAKER2) >>>>> using the `est_gff` param >>>>> 3) Specify gff file containing protein2genome results (computed using >>>>> MAKER2) using the `protein_gff` param >>>>> 4) Specify the genome fasta sequence file using the `genome` param >>>>> >>>>> I recently configured MAKER 2.27b to work using MPI and I tried launching >>>>> one contig (chromosome) on a compute node spawning 12 processes like so: >>>>> mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl >>>>> maker_exe.ctl 2>&1 | tee maker.err >>>>> >>>>> Side note: Without MPI, it works fine but takes very very long to >>>>> complete running on one chromosome (since it is going through the chunks >>>>> serially). >>>>> >>>>> On inspecting the `maker.err` file, I see server error messages that say >>>>> `DBD::SQLite::db do failed: database is locked`. On referring to a >>>>> previous email thread on the `maker-devel` mailing list, I see that Carson >>>>> had replied to the person with a similar issue asking them to check if the >>>>> working directory and TMP directory are being mounted on an NFS filesystem >>>>> because this is a potential problem with SQLite databases. >>>>> >>>>> Based on that suggestion, I switched the TMP directory to use a local >>>>> filesytem but the working directory is still NFS mounted. Despite that, I >>>>> still get this error. The previous email thread had no resolution for this >>>>> issue. My question is, should the working directory be local as well? I >>>>> see that despite setting the `TMP` variable, the SQLite DB is getting >>>>> created in the working directory. >>>>> >>>>> What might be the issue? >>>>> >>>>> Also, apart from this one error, I notice another error: >>>>> ERROR: Non-unique top level ID for chr5:hit:1454:4_0 >>>>> While this is technically legal in GFF3, it usually >>>>> indicates a poorly fomatted GFF3 file (perhaps you >>>>> tried to merge two GFF3 files without accounting for >>>>> unique IDs). MAKER will not handle these correctly. >>>>> >>>>> On inspecting the input GFF file (protein2genome), I see that this ID is >>>>> never repeated. So I have no idea whats going on here either. Any >>>>> suggestions? >>>>> >>>>> Below is my `maker.err` file from the run. (Dropbox link) >>>>> >>>>> Thank you very much. >>>>> Best, >>>>> >>>>> Vivek >>>>> >>>>> -- >>>>> Vivek Krishnakumar >>>>> vkrishnakumar at jcvi.org >>>>> >>>>> >>>>> >>>>> I've linked 1 file to this email: >>>>> >>>>> >>>>> maker.err (97.7 MB)Dropbox >>>>> http://db.tt/2tYyKCD7 >>>>> >>>>> >>>>> Mozilla Thunderbird makes it easy to >>>>> share large files over email. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> _______________________________________________ maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >>> >> >> >> >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 641 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Preview.app Document Type: image/png Size: 1205 bytes Desc: not available URL: From ranjani at uga.edu Thu Jan 24 22:17:13 2013 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Fri, 25 Jan 2013 05:17:13 +0000 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: References: , Message-ID: I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam > Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" > Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 11:43:17 2013 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2013 13:43:17 -0500 Subject: [maker-devel] Transcriptome data to gene models In-Reply-To: Message-ID: Also since single exon ESTs are almost always coming from background transcription and not real genes, MAKER may also require some sort of protein alignment or ab initio predictor support before promoting them to gene models. --Carson From: Sivaranjani Namasivayam Date: Friday, 25 January, 2013 12:17 AM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] Transcriptome data to gene models I did set the single_exon to 1, in spite of that I noticed that may single exon transcripts don't have gene models. I will check for other factors like small ORFs etc, I wanted to use the est2genome just to generate quick and gene models. Thanks for the information! From: Carson Holt [carsonhh at gmail.com] Sent: Wednesday, January 23, 2013 9:59 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] Transcriptome data to gene models est2genome is really only suitable for building a training dataset for building HMMS that will be used in a full maker run, and is not recommended for anything else. This is because most EST type alignments tend to be partial. MAKER does not try and extend these models, it just leaves them as is, so you will end up with a lot of partial gene models. MAKER will reject est2genome models if they do not have splice sites (unless single_exon is set to 1). MAKER will also not instantiate a model if the ORF is too small a percentage of the transcript. Using something like apollo, you can drag an est2genome alignment into the annotation tier and see what the model would have looked like if instantiated. You will probably see that for the ones that don't produce a gene model that they either have non-canonical splice sites or the longest open reading frame is short. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 16 January, 2013 9:16 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Transcriptome data to gene models Hi, I want to generate gene models for all my transcripts (based on just the transcript evidence). To do this I set 'est2genome to gene models' attribute to 1. I have disabled gene predictions from any another sources, that is, I do not provide protein data and turned off all gene predictors But I find gene models are not generated for all transcripts only about half of them. Can you tell me how maker decides which transcripts to predict models for, that is, how is it making this selective decision? Thanks, Ranjani _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Tue Jan 29 09:50:24 2013 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 29 Jan 2013 09:50:24 -0700 Subject: [maker-devel] Fwd: Help in installation of MAKER2 References: Message-ID: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 09:57:25 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 11:57:25 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: If it is a 64 bit Intel Mac make sure you install the 64 bit version of fink and not the 32 bit version. Then use fink to install both of these --> glib2-dev glib2-shlibs Installing them any other way on a Mac makes it so much harder to get the configuration right. Do 'fink remove' if you've already installed them with fink, then update fink and make sure it is the right fink for your processor before reinstalling. --Carson From: Barry Moore Date: Tuesday, 29 January, 2013 11:50 AM To: Maker Mailing List Cc: Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Jan 29 09:58:57 2013 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 29 Jan 2013 16:58:57 +0000 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> References: , <2B7D29A5-BB8D-408C-B037-F63FCEE3AC1E@genetics.utah.edu> Message-ID: Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 Date: January 29, 2013 4:45:49 AM MST To: > Hi Barry, I am trying to install Exonerate with no luck. I tried to join the Google group but I cannot post (I don't know why) there so I write directly to you. I used the info in google groups to install Exonerate in my Mac OS 10.6. Everything went fine (at least it looked like) until the configure step, when I have this error message: checking for socklen_t... yes checking for pkg-config... no ERROR: Could not find pkg-config ... is glib-2 installed ??? macpro:exonerate-2.2.0 admin$ pkg-get -bash: pkg-get: command not found I installed glib 1 and glib 2. But still the thing is not capable to get installed. I don't know what else to do. No way to use maker without exonerate, I guess... A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jan 29 10:04:54 2013 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 29 Jan 2013 12:04:54 -0500 Subject: [maker-devel] Fwd: Help in installation of MAKER2 In-Reply-To: Message-ID: I had problems moving from OS X 10.5 to 10.6 and from 10.6 to 10.7. All of which were solved by reinstalling fink (for the right processor ? 32bit vs 64bit) and all tools and libraries I had from fink. Thanks, Carson From: Daniel Ence Date: Tuesday, 29 January, 2013 11:58 AM To: Maker Mailing List , Carson Holt Cc: "alexmendozasoler at gmail.com" Subject: RE: [maker-devel] Fwd: Help in installation of MAKER2 Carson, Could this be related to the OSX Lion's support for exonerate's c-libraries? I think I remember you saying there were some difficulties with that when you upgraded your computer. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [barry.moore at genetics.utah.edu] Sent: Tuesday, January 29, 2013 9:50 AM To: Maker Mailing List Cc: alexmendozasoler at gmail.com Subject: [maker-devel] Fwd: Help in installation of MAKER2 Hi Alex, I'm forwarding your question to the Maker mailing list in hopes that some other maker users may have recently encountered and solved the same exonerate/Mac install issues that you are encountering. Barry Begin forwarded message: > From: Alexandre Mendoza Soler > Subject: Help in installation of MAKER2 > Date: January 29, 2013 4:45:49 AM MST > To: > > Hi Barry, > > I am trying to install Exonerate with no luck. I tried to join the Google > group but I cannot post (I don't know why) there so I write directly to you. > > I used the info in google groups > 20mac/maker-devel/Fjb_23sOm3Q/BpR8c6wYiqYJ> to install Exonerate in my Mac OS > 10.6. Everything went fine (at least it looked like) until the configure step, > when I have this error message: > checking for socklen_t... yes > checking for pkg-config... no > ERROR: Could not find pkg-config ... is glib-2 installed ??? > macpro:exonerate-2.2.0 admin$ pkg-get > -bash: pkg-get: command not found > > I installed glib 1 and glib 2. But still the thing is not capable to get > installed. I don't know what else to do. No way to use maker without > exonerate, I guess... > > A. Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: